Medical Software

Battle of the EHRs: athenaHealth vs Cerner

Published by in Medical Software

athenaHealth and Cerner are both extremely popular electronic medical records software options. athenaHealth is number 13 and Cerner is number 7 on our Top 20 Most Popular EHR Software rankings.

Both are full-featured, offering practice management functionality including appointment management, a patient portal, e-prescribing, and E/M coding. They both offer voice recognition for easier charting. And of course they are both HIPAA compliant, certified for Meaningful Use, and ONC-ATCB certified.

Both offer extensive training and onboarding help, including documentation, webinars, and live online and in-person training. Whereas athenaHealth is SaaS-only, Cerner can be installed locally or run in the cloud. I would not recommend using Cerner or any EHR offline, but it’s an option.

athenaHealth vs Cerner


athenaHealth offers online customer support only during business hours and Cerner offers 24/7 live support.

One Software Advice reviewer glowed that Cerner offers a “great support team.” Another wrote, “The support staff has been very helpful.”

Capterra reviewers also gave props to athenaHealth’s support staff, calling the team “well trained and very very polite, patient and professional.” The same reviewer listed under the “Cons” section: “They do not have an office in my hometown where I can go to work for them.” Calm down, Reginald.

“They are more than a software vendor. They have a staff that is full of knowledgeable professionals that can assist in every facet of our practice. They were the best source for making the transition from ICD9 to ICD 10. They are able to assist in every facet of our practice by dealing with both software issues and or Best Practice Management.”


Executives polled by HealthcareITNews cited improved UI most as the feature most likely to be effective at encouraging EHR use, and 47 percent put it in the number-one spot.

So, which has better UI?

A new report from KLAS has athenaHealth ranked just above Cerner in usability according to care managers, program administrators, and clinicians at the point of care.

Software Advice reviewers complained that Cerner’s UI was “Not as intuitive as I would like.” The same reviewer who said the support staff had been very helpful followed that up with, “Without them standing behind the doctors and nurses charting on this system would be impossible. This system could actually push physicians to early retirement..” It is, in this reviewer’s estimation, “extremely difficult to navigate,” and “takes away from patient care.” They go on, “I’ve used an EMR in my office for 14 years and this new system is unbelievably cumbersome and non-intuitive.”

Another wrote, “The software is poorly designed, difficult to navigate, and generally feels like it was designed by engineers who have never worked in a healthcare setting.” Ouch.

Capterra reviewers were kinder to athenaHealth. From our friend Reginald: “The software is user-friendly.” Another reviewer wrote, “Even though it seemed overwhelming at first, it is actually pretty easy to use and get around on.” Another reviewer wrote, “The charting is easy once you get your templates setup.” Maureen wrote that athenaHealth is “Very easy to navigate.”

Integrations and Interoperability

“Interoperability is at least as important as functionality” for EMR systems, Michael Gagnon told Healthcare Dive. The CTO at Vermont Information Technology Leaders also recommended providers emphasize interoperability when choosing between vendors. You want to buy the system you’ll need next year and the year after that. An extensible system is much more useful going forward.

And it’s certainly true that your EHR won’t do you much good if people in your organization refuse to fully embrace it. HealthcareITNews polled 95 healthcare executives in October 2016 about strategies they thought would be effective at enticing their physicians and nurses to use their EHR. Integrating their EHRs with other technologies was what 60% of respondents said they’d do in 2017 to boost adoption.  

When HealthcareITNews asked healthcare executives what types of interoperability projects healthcare organizations will be working on in 2017, 65 percent included connecting to external databases, such as health information exchanges. Connecting applications within the organization was on this list for 58 percent. And 37 percent included adding connections from medical devices to existing systems.

athenaHealth offers pre-built integrations for applications, diagnostic testing systems, external health systems, and public health entities. It also offers an API (and other tools) for custom integrations.

Cerner is also committed to integration, it’s built three platforms to integrate with each other and with external systems to connect clinical, operational, and financial data. In an interview at HIMSS17, Cerner President Zane Burke indicated they’re making efforts to create application program interfaces (APIs) which will increase interoperability not just with other EHRs but with other third-party software and apps too for mHealth, population health, and information exchange.

Value-based care

According to HealthcareITNews, 40 percent of execs say that more of their staff will use the EHR if they can demonstrate how it can help with managing value-based care. John Halamka, MD, CIO at Beth Israel Deaconess System and a professor of medicine at Harvard University spoke to HealthcareITNews about why that might be.

“When you look at the quality programs and MIPS and MACRA, suddenly you are seeing a realignment of incentives where doctors are paid for wellness and quality as opposed to quantity,” Halamka said. “Unless you are collecting data about patients across the population, it’s really hard to control expenses, enhance quality and improve workflow. EHRs were put in basically as dumb data communication systems without emphasis on exchange and workflow. But because of payment reform, we have incentives to do data exchange. Different things are bubbling to the top.”

So are athenaHealth and Cerner collecting data about patients across the population?

athenaHealth CEO and President Jonathan Bush is certainly trying.

“After you start using artificial intelligence to get the lame and lonely work out of the doctor’s life, you start to form clinical conclusions,” Bush told Healthcare Dive. “Because we’ve got everybody streamed through one instance of one application, we can start to see consistencies and inconsistencies in order choices, in patient compliance and what doctors are doing about it. We’re starting to just now get insight into clinical practices that work and don’t work through bio-surveillance and watching what goes on in our network. I think over the years, that will be the biggest deal about athena.”

In the company’s 2016 full-year SEC filing, Bush wrote, “Our expanding network now connects care across nearly 88,000 providers, nearly 86 million patients, and over 143,000 network endpoints.”  

In February, the company announced three initial efforts for 2017:

  1. Reduce pregnancy-related medication safety risks
  2. Help with the opioid crisis by improving chronic pain management
  3. Improve cholesterol treatment for cardiovascular patients

However, for all its effort, the KLAS report puts Cerner above athenaHealth in how likely you are to find it easy to implement population health tools. Yet KLAS praised athenaHealth in the report for admirable population health management skills among EHRs, writing that when it comes to data integration, for example, customers say that athenaHealth handles the dirty work, especially when it comes to complicated, unstructured claims data.

But, obviously, the more data your tools have access to, the better. And according to the report, “Among fully rated PHM vendors, athenaHealth, Optum, and Philips Wellcentive have the highest percentage of customers merging both clinical data from EMRs and claims data from payers.” But Cerner is no slouch, with about half of its customers pulling data from three non-Cerner EHRs on average. More than two-thirds of Cerner’s customers take in claims data from four payers each, on average.


One reviewer described athenaHealth’s reporting module as “great and robust” writing that it was “especially helpful for practices attesting for meaningful use and PCMH.” However, pulling this report requires creating a ticket for customer service which “takes a long time to get answered.” But another disagreed, saying “Reports are easy to create and don’t take forever generating!”


In 2018 healthcare providers must use the 2015 edition of their EHRs in order to qualify for incentives under MACRA’s Merit-based Incentive Payment System or Stage 3 of Meaningful Use. According to Politico, neither athenaHealth nor Cerner are on the ONC’s list of 2015 EHRs. However, a spokeswoman told Politico that Cerner will begin testing with ONC in March 2017.


athenaHealth is a great choice if you want a user-friendly interface, great reporting, and you only need support during business hours. athenaHealth has a lot planned for population health management, but right now Cerner has the leg up, except when it comes to hand-holding during integration. To learn more, athenaHealth offers a free demo.

Cerner is the best option for HDOs that need access to support 24/7, extreme extensivity, and better population health management functionality, at least for now.

I want to end with some great advice from our old friend Reginald. The last section on Capterra’s review form is “Recommendations to other buyers.” In this section, Reggie gave up some awesome advice for all EHR buyers. “Do not hesitate to call and ask for help if you are sure about something,” Reginald wrote. “There are many bells and whistle available to make your job easy. You should stop to see if there may be a shortcut to an operation and there usually is something that can make your job easier.”

Looking for Medical Practice Management software? Check out Capterra's list of the best Medical Practice Management software solutions.

About the Author

Cathy Reisenwitz

Cathy Reisenwitz

Cathy Reisenwitz is a former Capterra analyst.


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