Introduction: The Big Fourth-Quarter Scramble

On October 16, 2015, the Centers for Medicare and Medicaid Services (“CMS”) and the Office of the National Coordinator for Health Information Technology (“ONC”) published in the Federal Register a final rule (the “Final Rule”) with a twofold purpose: to establish the requirements for participation in Stage 3 of the Medicare and Medicaid Electronic Health Records (“EHR”) Incentive Programs; and, of more immediate concern to many eligible professionals (“EPs”) and eligible hospitals, to implement significant changes to Stages 1 and 2 of Meaningful Use. Specifically, the Final Rule combines Stage 1 and Stage 2 into a single “Modified Stage 2.”1 This alert will focus on the requirements of Modified Stage 2.

The issuance of Modified Stage 2 has sent providers scrambling, as many had already begun a 90-day EHR reporting period on October 1, 2015 (CMS is allowing all EPs and eligible hospitals, irrespective of Stage of Meaningful Use, to use a 90-day reporting period in 2015). Providers who had begun the fourth quarter of 2015 under the old Stage 1/Stage 2 rubric are now tasked with meeting new standards (and, in some cases, new measures altogether) in short order. With only a few weeks left in 2015, CMS is continuing to release new resources to help providers comply with the requirements of Modified Stage 2.2These eleventh hour updates underscore the general state of confusion among providers and the difficulties associated with complying with the new requirements of Modified Stage 2.

Will More Providers Apply for Hardship Exceptions?

Shortly following the release of the Final Rule, CMS issued a response to a “Frequently Asked Question” (FAQ), stating that if a provider is unable to meet the requirements of Modified Stage 2 in 2015 due to the timing of the Final Rule, the provider may apply for a hardship exception in an effort to avoid penalties for the 2015 reporting year.3 While hardship exceptions are not guaranteed and will be reviewed on a case-by-case basis, CMS stated that it has approved 85 percent of the hardship exception applications received to date.4 For those providers that do plan to attest to Modified Stage 2, however, understanding the modified criteria, as well as the availability of certain “alternate” exclusions or measures, is a time-critical task.

Will the New “Alternate Exclusions” Be a Life Raft?

Recognizing that providers scheduled to report in Stage 1 or Stage 2 for the 2015 reporting year may face significant burdens in meeting the Modified Stage 2 requirements, and moreover that the hasty implementation of additional certified electronic health record technology (CEHRT) modules or functionalities could pose a risk to patient safety and clinical workflows, CMS has implemented “alternate” exclusions and specifications for Stage 1, and, in some instances Stage 2, providers. These alternate exclusions, at least for Stage 1 providers, are generally structured in one of two ways: (i) where a Modified Stage 2 measure imposes a higher threshold than the prior rule, the Stage 1 provider may utilize the Stage 1 threshold from the prior rule, or (ii) where Modified Stage 2 includes a measure for which there is no Stage 1 equivalent, the Stage 1 provider may exclude the measure. Alternate exclusions are not available for all Modified Stage 2 measures, however.

While most “alternate exclusions” contained in the Final Rule apply to providers scheduled to report in Stage 1 for the 2015 reporting period, CMS has made certain alternate exclusions applicable to the public health reporting measures available to Stage 2 providers as well. Throughout this alert, we will highlight in bold where an alternate exclusion might be available for the new Modified Stage 2 criteria that we are discussing. This alert cannot cover all of the new Modified Stage 2 criteria, but we will address some of the more significant changes, as well as those instances in which an alternate exclusion might apply with respect to the modified standard.

Overview of Modified Stage 2

In Modified Stage 2, CMS eliminated the distinction between “core” and “menu” set objectives in favor of a single set of 10 objectives for EPs and nine for eligible hospitals.5 This shift was intended to realign the criteria for Stages 1 and 2 with the end-goal of the EHR Incentive Program, which is to establish a sustainable framework for Meaningful Use, to reduce the overall reporting burden on providers and to achieve interoperability.6 In furtherance of the goal to streamline the reporting requirements, CMS eliminated a number of objectives and measures determined to be redundant, duplicative of more advanced measures, or “topped out” (meaning that based on provider performance, the objective and/or measure has already achieved widespread adoption). These “topped out” measures include many of the data-entry objectives such as record smoking status, record vital signs and structured lab results. While these are no longer required for Meaningful Use, CMS encourages providers to continue these activities as best practices.

Among the more significant changes imposed by Modified Stage 2 are the following: (i) modifying the patient engagement requirements of the “patient access” Stage 2 objectives; (ii) imposing new standards for public health reporting; and (iii) implementing changes to certain foundational objectives to align with CMS’ goal of the “advanced use” of EHR technology by 2018. These changes are described in more detail below.

Patient Access Measures – CMS Lowers Patient Engagement Thresholds

Providers scheduled to be in Stage 2

Stage 2 of Meaningful Use under the prior rule included two core objectives aimed at facilitating patients’ access to their own health information: patient electronic access and secure messaging (EPs only). Satisfying the measures for each of these objectives depended in part on patient engagement. For example, the second measure for “patient electronic access” required that more than five percent of patients discharged from the hospital view, download or transmit to a third party their information. Similarly, the “secure messaging” objective required that more than five percent of the EP’s patients seen during the reporting period send a secure electronic message to the EP using CEHRT. In response to these objectives, many commenters expressed concerns about the lack of infrastructure and preparedness to meet these thresholds, often for reasons outside the provider’s control – such as patients lacking web access or being reluctant to utilize patient portals out of unfamiliarity and distrust of privacy controls.

While continuing to support and prioritize advancing patient electronic access to health information, CMS has recognized in the Final Rule that the Stage 2 measures lack flexibility and “includ[e] only patient-initiated communication rather than provider-driven engagement,” thereby failing to promote a wide range of use.7 Accordingly, CMS has lowered the patient engagement thresholds for years 2015 and 2016 of Modified Stage 2. For the “patient electronic access” objective, the second measure may be met if at least one patient seen by the EP during the reporting period views, downloads or transmits his or her health information. The “secure messaging” measure may be met in 2015 by demonstrating that the capability to send secure messages with the EP was fully enabled, and in 2016 by demonstrating that at least one patient seen by the EP during the EHR reporting period sent a secure message using CEHRT to the EP.8

Providers scheduled to be in Stage 1 in 2015

Recognizing that providers scheduled to be in Stage 1 for 2015 may face difficulty in meeting the patient engagement measures that were not required in Stage 1 (Stage 1 required only that patients have the “ability” to access their data online), CMS has implemented an alternate exclusion for the second measure of the “patient electronic access” objective and for the “secure messaging” objective, which may be claimed if the EP was scheduled to demonstrate Stage 1 for a 2015 EHR reporting period. This alternative exclusion recognizes that the prior version of Stage 1 did not contain an equivalent measure that would have required any patients to view, download or transmit to a third party their information or to send a secure message.

Modifications to Build Toward “Advanced Use” of EHR Technology

CMS has previously identified eight key policy areas representing the “advanced use” of EHR technology, consistent with the directives of the HITECH Act.9 These eight policy areas form the basis of the Meaningful Use Stage 3 objectives and measures. Consistent with these goals, CMS has imposed changes in Modified Stage 2 to certain of these eight foundational objectives designed to better prepare providers for the reporting requirements in Stage 3. While “patient access” and public health registry reporting are discussed elsewhere in this summary, certain other noteworthy changes to the foundational objectives are briefly summarized below.

  • Protect patient health information. CMS has modified the objective requiring providers to conduct a HIPAA security risk analysis to specifically require that the analysis address encryption of protected health information maintained in CEHRT. CMS has further clarified that the risk analysis may be conducted outside the EHR reporting period, but must be conducted within the same calendar year as the reporting period (and prior to date of attestation, if attesting prior to end of calendar year).
  • Clinical decision support. This Modified Stage 2 objective consolidates two Stage 1 core objectives (clinical decision support rules and drug-allergy checks) into one objective with two measures, with the goal of allowing providers the discretion to select the most appropriate clinical decision support rules to improve patient performance on significant health conditions. Notably, the first measure of this objective requires that the EP or eligible hospital implement five clinical decision support interventions related to four or more of the clinical quality measures relevant to the EP or hospital’s patient population. An EP or eligible hospital scheduled to be in Stage 1 in 2015 may select an alternate measure, requiring the implementation of one clinical decision support rule.
  • Electronic prescribing. The Modified Stage 2 measure advances Stage 1 standards by requiring that more than 50 percent of permissible prescriptions written by the EP be queried for a drug formulary, in addition to being transmitted electronically using CEHRT. Though CMS received comments expressing concern with the added burden to include a query for the drug formulary, this requirement was finalized. Recognizing the burden on providers to take additional action in this regard, CMS has offered two allowances. First, providers may count a patient in the numerator where no formulary is available to conduct a query. Second, if a query would require additional action outside the capabilities of the provider’s CEHRT, the provider is not required to take any further action (and may count such encounters in the numerator). CMS has provided alternate exclusions and/or measures for EPs and eligible hospitals scheduled to be in Stage 1 in 2015. Essentially, the alternate standard allows the EP or hospital to rely on the prior Stage 1 measure.
  • Computerized Provider Order Entry (CPOE).
    • Providers scheduled to be in Stage 2. Modified Stage 2 adopts the previous Stage 2 structure of three distinct measures and a separate required threshold for each type of order: (i) medication, (ii) laboratory, and (iii) radiology. CMS has retained the Stage 2 thresholds for each type of order: 60 percent for medication, and 30 percent for each of radiology and laboratory.
    • Providers scheduled to be in Stage 1 in 2015. CMS has provided both alternate measures and alternate exclusions for providers scheduled to be in Stage 1 in 2015. Specifically, providers scheduled to be in Stage 1 may attest to the prior Stage 1 measure with respect to Measure 1 (medication), and, with respect to Measures 2 and 3 (radiology and laboratory), may claim an alternate exclusion. In response to ongoing stakeholder questions about whether scribes qualify as “medical staff” qualified to enter orders for purposes of CPOE, CMS reiterated, “in general, scribes are not included as medical staff that may enter orders for purposes of the CPOE objective[; h]owever, we note that this policy is not specific to a job title but to the appropriate medical training, knowledge, and experience.” For example, CMS defers to providers to determine the proper qualifications and training for the medical staff entering orders, but states medical staff must be credentialed to perform duties equivalent to a medical assistant and “must have at least a certain level of medical training in order to execute the related CDS for a CPOE order entry.”10
  • Health Information Exchange.
    • Providers scheduled to be in Stage 2. Previously captured by the “summary of care” core or “menu” objectives in Stage 1 (2014) and Stage 2, the “health information exchange” objective for Modified Stage 2 requires that an EP or eligible hospital that transitions or refers a patient to another setting of care or provider of care must use CEHRT to create the summary of care record and transmit the summary electronically for more than 10 percent of transitions of care and referrals. Providers remain concerned about meeting this objective based on a lack of control of other providers, as well as a lack of participation by specialists receiving referrals. For example, a provider may refer or transition patients to another provider who is able to claim the exclusion for making fewer than 100 referrals and who accordingly is reluctant to participate.Despite these concerns, however, CMS did not reduce the 10 percent threshold or otherwise alter the measure as finalized. However, CMS did potentially allow for some flexibility. CMS clarified the definition of “transition of care” to mean a transition “where the referring provider is under a different billing identity within the Medicare and Medicaid EHR Incentive Programs than the receiving provider and where the providers do not share access to the EHR.” Where providers do share access to an EHR, however, a transition or referral may still count toward the measure “if the referring provider creates the summary of care document using CEHRT and sends the summary of care document electronically.”11 If a provider chooses to include such transitions to providers where access to the EHR is shared, the provider must do so universally for all patient and all transitions or referrals. For example, if a provider shares an EHR with a hospital and also with a skilled nursing facility, the provider would be prevented from including only the shared EHR referrals and transitions from the hospital.
    • Providers scheduled to be in Stage 1. CMS has implemented an alternate exclusion that may be claimed if the provider was scheduled to demonstrate Stage 1 for a 2015 EHR reporting period. This alternative exclusion recognizes that the prior version of Stage 1 did not contain an equivalent measure.

Public Health Reporting – Confusion Abounds as Former “Menu” Objectives Become Mandatory

In those cases in which the public health reporting objectives have, prior to the Final Rule, been voluntary “menu” objectives (or, in the case of Stage 2, partially “core” and partially “menu” objectives), Modified Stage 2 effectively makes public health reporting a requirement for all providers. Not surprisingly, because the measures associated with this objective require registration and coordination with state-run agencies, advance planning, many providers have been concerned in the wake of the Final Rule with their ability to meet the new standards of reporting.

Specifically, in Modified Stage 2, CMS has consolidated the proposed public health reporting categories into three final measures for EPs, i.e., immunization registry, syndromic surveillance and specialized registry (to include a cancer registry), and into four final measures for eligible hospitals, i.e., immunization registry, syndromic surveillance, specialized registry (to include a cancer registry) and laboratory results. Intending to resolve confusion about the prior “ongoing submission” requirements for public health reporting in Stages 1 and 2, CMS has implemented a new standard of “active engagement” to better reflect the communications between reporting providers and the data registries.12 An attesting provider may demonstrate “active engagement” in three alternative ways: (i) completing registration to submit data; (ii) testing and validation; or (iii) electronically submitting production data.

Anticipating provider concerns about meeting this new standard, CMS has clarified that “any action which would be acceptable under the Stage 1 and Stage 2 public health reporting objectives would fit within the definition of the “active engagement” options.”13 For example, CMS stated in an FAQ released on November 17, 2015 that providers who were scheduled to be in Stage 1 in 2015 may meet the “testing and validation” option by having sent a test message to the applicable registry.14 CMS specifically confirmed that such providers would not have to file a registration of intent to submit data to the applicable registry. CMS noted, again, that “we did not intend to require providers to engage in new activities during 2015, which may not be feasible after the publication of the final rule in order to successfully demonstrate meaningful use in 2015.”15

Still, providers that had not planned to report on a previously voluntary “menu” public health objective could face challenges. Fortunately, for Modified Stage 2, CMS has promulgated an alternate specification whereby an EP scheduled to be in Stage 1 in 2015 may meet one measure instead of all three measures (and whereby an eligible hospital may meet two measures instead of four). CMS has also preserved the ability of any provider, irrespective of Stage of Meaningful Use, to claim an applicable exclusion from all available measures (including through a combination of “regular” and new “alternate” exclusions as discussed below), meaning that an EP could be excluded from each of the three reporting measures or an eligible hospital could be excluded from each of the four reporting measures.16

On October 22, 2015 an FAQ published by CMS established a new “alternate exclusion” that EPs, hospitals, and CAHs may utilize (in addition to the regular exclusions) for public health reporting objectives in 2015.17 This new “alternate” exclusion applies to both Stage 1 and Stage 2 providers and can be claimed if the provider “did not intend to attest to the equivalent prior menu objective consistent with [CMS’] policy for other objectives and measures . . . .”

  • Providers scheduled to be in Stage 1 in 2015. CMS stated in the FAQ that EPs scheduled to attest to Stage 1 in 2015 may claim an “alternate exclusion” for up to two measures while either meeting or claiming the “regular” exclusion for the third measure. Eligible hospitals scheduled to be in Stage 1 in 2015 may claim an “alternate exclusion” for up to three measures while either meeting or claiming the “regular” exclusion for the fourth measure.
  • Providers scheduled to be in Stage 2 in 2015. EPs scheduled to attest to Stage 2 in 2015 may claim an “alternate exclusion” for only one measure (either Measure 2 (syndromic surveillance) or Measure 3 (specialized registry reporting)) while either meeting or claiming the “regular” exclusion for the other measures. Eligible hospitals scheduled to be in Stage 2 in 2015 may claim an “alternate exclusion” for only one measure (Measure 3 (specialized registry reporting)) while either meeting or claiming the “regular” exclusion for the other measures.

Timeline of Meaningful Use: Deadlines for Attestation and Payment Adjustments for 2015

Several changes imposed by the Final Rule were aimed at streamlining the reporting and attestation processes, as well as easing the reporting burden in light of implementing Modified Stage 2. Starting in 2015, the EHR reporting period shifts to the calendar year for eligible hospitals, now aligned with the EP reporting period. For 2015 only, all providers may utilize a 90-day reporting period. Further, eligible hospitals may select, as such reporting period, any continuous 90-day period between October 1, 2014 (previously the start of the FY 2015 payment year for hospitals) and December 31, 2015.

All providers have until February 29, 2016 to attest to Meaningful Use for 2015. Because CMS needs time to update the attestation process in light of the Modified Stage 2 changes, attestation will not be open until January 4, 2016.

What’s Next?

Many providers are likely preoccupied with ensuring they can meet the Modified Stage 2 measures (or applicable exclusions) in the next several months. However, providers should be aware that CMS has allowed a 60-day comment period commencing with the Final Rule (ending December 15, 2015). Providers are encouraged to submit comments, as CMS has previously indicated that it will use commenters’ feedback to inform future policy developments for the EHR Incentive Programs, and may even consider changes subsequent to the Final Rule.18


1 See 80 Fed. Reg. 62762 (October 16, 2015).

2 Per an email sent December 4, 2015, CMS states it has posted additional resources on the CMS EHR Incentive Programs website. available at

3 See FAQ #14285, available at

4 Id.

5 See for a helpful chart giving an overview of Modified Stage 2.

6 See Proposed Rule, Medicare and Medicaid Programs; Electronic Health Record Incentive Program – Stage 3, 80 Fed. Reg. 16732 (March 30, 2015).

7 See 80 Fed. Reg. 62815 – 62817.

8 Note that the objectives and measures revert to the prior Stage 2 thresholds in Stage 3.

9 See 80 Fed. Reg. 16743.

10 80 Fed. Reg. 62798.

11 Id. at 62806.

12 80 Fed. Reg. 62824-62825.

13 80 Fed. Reg. 62819.

14 See FAQ # 12409, available at

15 Id.

16 80 Fed. Reg. 62820; 62824.

17 See FAQ # 12985, available at

18 Comments may be submitted via the following link:!documentDetail;D=CMS-2015-0033-0767.