One of our small Allscripts practices recently made the decision to move to AthenaHealth, and Physician Interlink had the opportunity to assist in the migration and to continue to “do the work AthenaHealth does not do.” The practice, consisting of two physicians, has been a revenue cycle management client since the early 2000’s; first on a legacy system we provided, and then on Allscripts in the Saas hosted environment, where we provided virtual services. The change to Athena was prompted by their participation in MIPS, and the hope that one of the physicians would find the EHR easier to use, would have an easier time navigating a visit from beginning to end, and could sign off timely on visits. This article is a side-by-side comparison of the PM functions of the systems, and our experience working with both.

Apples and Oranges?

At first glance, the two systems appear to be from different universes. Allscripts is a conglomeration of multiple software packages and services put together over time to perform the billing function. The EHR is a separate application and database with key interfaces to the PM. Within the PM, the modules are separate, meaning there are, for instance, very few places where you can click on a claim and be able to do something else. AthenaHealth looks and feels much more like it was “built from the ground up.” It is visually appealing and was built for a tech-savvy user. It was not built in a “compartmentalized” fashion. There are links throughout, including within reports to get back to source data. That said, it is easy to “lose” claims in the process. Also, reading and understanding a patient account is cumbersome.

Another difference between the two systems is their respective hosting configurations. Allscripts can be hosted remotely, deployed in a medical office, and there is a cloud solution using published apps. AthenaHealth is a web-based system.

AthenaHealth also performs some of the functions of billing, such as sending claims, limited claims follow-up, and posting payments.


The approach to implementation by the two companies is vastly different. AthenaHealth uses a virtual approach, while Allscripts uses live implementation coordinators. Athena has built an expansive library of knowledge, including training videos that cover every area for every level of user. These videos are used extensively in implementation, with office employees watching hours of video training. System customization for AthenaHealth is done via Webex with an implementation specialist and key office personnel working through a series of instructional sessions and configuration tasks. Allscripts also assigns an implementation coordinator, but there is a combination of remote and onsite instruction and configuration. At go-live, Allscripts has an implementation coordinator onsite. AthenaHealth has a coordinator reachable by phone, or the practice has the option to pay extra for onsite help.

Daily Work – Charge Passing

Both systems generate charges when a visit is “signed off.” Those charges migrate to an import charges window in Allscripts where it is easy to scroll through and review all charges by line item. There are filters that allow pulling charges by date, provider and/or location. In AthenaHealth, charges are found in a work queue called “missing slips.” You can filter to get the ones that are reviewed by provider, which means they are ready to bill. You can’t see the charge, though, without clicking on it. Both systems have claim scrubbers and allow editing of a charge. However, only Allscripts allows multiple charges to be brought in at the same time, which for simple charges that really don’t need editing, saves lots of time. The Allscripts claim scrubber allows for custom edits, where needed. Athena Health’s rules engine produces some incorrect results, and the process to have corrections made is cumbersome.

Daily Work — Claims Processing

AthenaHealth seamlessly handles claims processing and issues that are typically found at the clearinghouse level, and are returned to the practice in a work queue for corrections to be made. With Allscripts, the clearinghouse is an external entity, and practices must log in daily on the clearinghouse’s website to check for claims returned or for issues to correct.

Daily Work – Payment Posting

AthenaHealth handles payment posting for the practice. Issues are returned to the practice in a work queue to fix. Problems arise where there are nonstandard or unacceptable payments, getting virtual credit cards to post while they are still active, and determining what AthenaHealth does with zero-pays. While practices do this work in Allscripts, the remittance auto-posting is very customizable by remittance advice reason and remark codes by payor, assuring nothing is written off that actually should be corrected or appealed. Athena does provide an area where you may search for zero-pays to determine if write-offs were correct, or in error.

Daily Work – Denials

AthenaHealth comes with preloaded denial work queues, which may be customized by the user. Allscripts also has customizable work queues for unpaid claims and denials. AthenaHealth had developed “kick codes,” which are roughly 100 codes that must be attached to any reworked claim to let AthenaHealth know what to do with the claim. Choosing the incorrect kick code can keep the claim in a hold status. Therefore, using kick codes is an extra step that practices must learn and incorporate into their workflow. Creating corrected claims is a multi-step process in Athena. AthenaHealth does some claim follow-up. However, they do have what they call “Endpoints” where they stop any action. Practices are welcome to continue work on their own at that point. We have found the denial work takes about the same amount of time in both systems, with about the same volume of claims. We do not have fewer claims to work with AthenaHealth.


AthenaHealth has very good Help windows (“AthenaNet O Help”) that are integrated in the program modules and can be accessed in each module with help for that area. In addition, there are training videos and a Resource center. Allscripts also has similar help topics, but they are not integrated in each program module, and are organized by topic in a separate help area. Both companies allow online logging of support issues or call-in logging. How these companies handle live support is a reflection on corporate philosophy. Allscripts is very hands-on with live, experienced techs calling or emailing back on support cases, usually the same day the case is logged. These techs work with the client to solve the issue. If the issue can’t be solved immediately, they access whatever support they need to stay involved daily until the case is resolved. AthenaHealth is not so hands-on. As an example, you may be referred to a video or article to gain the knowledge you need to solve your problem. At times, the AthenaHealth techs will walk you through a solution, but this is the exception.


The reporting modules are vastly different in the two systems. AthenaHealth does not have any pre-formatted reports. All reports can be run to the screen, but to print requires downloading in Excel and formatting. There are many more reporting options in Athena, though, which makes creating reports a complex process. To assure you are getting the data you think you are. Allscripts has approximately 15 pre-formatted reports that have simple selection criteria. Most of the reports can be exported as CSV files and manipulated. In addition, for more advanced users, data can be accessed via either Crystal or Excel for customized reporting.


My impression of AthenaHealth is it tries to be everything to everybody. They sell themselves as a full-service billing company, and that they handle all the billing functions. I find this not to be the case, however. They are a reasonable fit for a practice that already has billing expertise. Implementation for our small practice was virtual; this may not be the case for larger groups. It would be very important to determine what type of support is needed for implementation from a vendor. The support provided by AthenaHealth for our client simply was not adequate, and the conversion took much too long. We finally had to jump in and assist with EHR configuration to get to the point where we could go live, and charges would pass correctly. The system has not changed the amount of back-end work we do, and the physician, who had issues signing off, still has as many open charts.

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