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Best for: Pediatrics, Ambulatory CareBest for: Multi-Specialty, Acute Care
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When choosing the best electronic medical record (EMR) system, it’s essential to find one that can streamline workflows, ensure compliance, and improve overall practice efficiency. Two of the leading and prominent EMR options in the market are athenahealth and Cerner, both known for their comprehensive healthcare solutions and improving operational efficiency.

In this side-by-side comparison guide, we will explore their key features, pros and cons, and benefits to help you determine the system that suits your healthcare organization's current and future needs.

athenahealth Vs. Cerner: Head-On Comparison

athenahealth is a cloud-based healthcare IT platform designed primarily for ambulatory practices, offering integrated EHR and practice and revenue cycle management. It delivers streamlined workflows, patient engagement tools, and data-driven insights to optimize practice performance. Its interface is ideal for small to mid-sized practices, with its services being highly customizable to meet practice needs. Moreover, the platform has won four 2024 Best in KLAS awards across various categories.

On the other hand, Cerner EMR, now Oracle, is the second-largest U.S. EHR vendor by market share, serving 24.9% acute care hospitals and 25.8% beds as of 2022. Known for its strong interoperability and population health management capabilities, Cerner provides a platform that supports data sharing across networks and enhanced decision-making through advanced analytics. Its solutions are built to handle large-scale operations, making it a preferred choice for complex healthcare environments.

athenahealth Vs. Cerner: At A Glance

Feature

athenahealth

Cerner

Patient Engagement Tools

  • Patient portal
  • Telehealth
  • Payment tools
  • Electronic health record (EHR) systems
  • Population health management systems

Revenue Cycle Management

  • Integrated billing
  • Medical coding
  • Claims resolution tools
  • ASO billing (including stop-loss insurance)
  • HIPAA-compliant cloud solution

Practice Management

  • Scheduling and billing
  • Workflow automation
  • Scheduling
  • Patient tracking
  • Patient accounting

Integrations

  • athenahealth Marketplace
  • 800+ API endpoints
  • Application integration and low-code automation
  • API full lifecycle management
  • Oracle GoldenGate Kafka and event streaming

AI-Powered Tools

  • Generative AI
  • Generative AI
  • AI solutions hub

Support

  • Phone
  • Chat
  • Web
  • Email
  • Live chat
  • Call

Security And Compliance

  • Technical, administrative, and physical safeguards to protect data
  • HIPAA, HITECH/ARRA, ACA compliant
  • Cloud guard
  • Security Zones
  • Vulnerability Scanning

Telehealth

  • Customizable video window
  • Group video conferencing
  • Fully-embedded solution
  • Enterprise-level video visits
  • Oracle Health Scheduled Video Visits
  • Oracle Health Remote Patient Monitoring

athenahealth Vs. Cerner: Pros And Cons

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ProsPros
  • Specialty-focused workflows
  • Advanced healthcare analytics
  • Streamlines appointment scheduling
  • Resourceful patient portal
  • Reliable customer support 
  • Strong interoperability
  • Comprehensive clinical documentation tools
  • Efficient patient charting
  • Customizable to meet organizational needs
  • Offers training for in-house implementation
ConsCons
  • Occasional billing errors
  • Compatibility problems with a few software
  • Regular updates can interrupt workflow
  • Complex system, requiring training for users
  • System performance can slow down
  • Challenges with navigating certain features

athenahealth Vs. Cerner: Side By Side Comparison

As discussed, athenahealth and Cerner are leading EMR systems, offering unique features tailored to different healthcare needs. Below is a side-by-side comparison of six key features to help you determine which platform aligns with your practice.

Patient Portal

athenahealth provides a patient portal that allows patients to manage appointments, view medical records, and communicate with their healthcare providers. It also supports online bill payments via mobile devices, improving patient engagement.

Cerner’s patient portal, HealtheLife, enables patients to easily access their health information, including medications, lab results, and appointment. The software also integrates with other health systems, allowing for better continuity of care.

Winner: athenahealth takes the lead here for its ease of use and mobile payment options.

Appointment Scheduling

athenahealth simplifies appointment scheduling with self-service tools that integrate patient data and administrative workflows, enhancing management efficiency and improving patient satisfaction.

Cerner offers advanced scheduling features that are especially beneficial for large health systems. Using patient data, it recommends alternative appointments when preferred times are unavailable.

Winner: athenahealth wins this one for its user-friendly and flexible scheduling tools.

Interoperability

athenahealth offers interoperability through APIs and integrations with various health systems. Its marketplace allows third-party vendors to connect with its platform, promoting greater data exchange.

Cerner excels in interoperability, supporting large-scale data sharing across networks, especially through its Cerner Health Information Exchange (HIE), which is designed to connect different care facilities and providers.

Winner: Cerner takes the prize for its superior network-wide data exchange capabilities.

Revenue Cycle Management (RCM)

athenahealth integrates RCM tools that help practices manage billing, claims, and collections, offering a centralized dashboard to streamline operations and improve financial performance.

Cerner provides a comprehensive RCM solution suited for large health systems, enabling precise cost estimates and automated claims processing. It helps reduce administrative burdens while maximizing revenue.

Winner: This ends in a draw as both systems provide excellent RCM tools but cater to different practice sizes.

Telehealth

athenahealth offers a seamless, HIPAA-compliant telehealth solution that integrates directly into its platform. It includes video conferencing, billing support, and patient outreach tools for a complete telemedicine experience.

Cerner’s telehealth solutions are integrated within its broader suite of healthcare tools, offering virtual visits and remote monitoring capabilities, making it suitable for larger care networks.

Winner: athenahealth wins this round for its ease of integration and user-friendly telehealth tools.

Population Health Management

athenahealth provides tools to track and manage patient populations, focusing on improving patient outcomes and operational efficiency, particularly within ambulatory settings.

Cerner is highly regarded for its advanced population health management tools, which support large-scale patient tracking, predictive analytics, and data-driven decision-making.

Winner: Cerner is the leader for its in-depth capabilities to manage complex patient populations across large health systems.

athenahealth Vs. Cerner: Pricing Plans

athenahealth operates on a flexible, customized pricing model based on the organization’s revenue cycle and collections. This means costs can vary depending on patient volume and practice earnings, allowing healthcare organizations to manage expenses more effectively. athenahealth also promotes transparency by eliminating hidden fees and long-term contracts, giving practices the flexibility to opt-out at any time while retaining access to their data.

Similarly, Cerner (now Oracle Health) offers tailored pricing based on the specific needs of the healthcare organization. Like athenahealth, Cerner's pricing includes factors such as system customization, implementation, and ongoing support. However, the total cost can vary significantly depending on the size and complexity of the healthcare system being served.

athenahealth Vs. Cerner: What Users Have To Say?

athenahealth users frequently highlight its user-friendly design, which simplifies tasks like appointment scheduling and patient communication.

Many users have praised its billing and claims management tools, with one saying, “It improved our collections by a significant margin.”

However, some users mentioned occasional issues with system updates, particularly when updating patient insurance information.

Cerner, on the other hand, is well-regarded for its powerful data management capabilities.

One reviewer appreciated its comprehensive feature list, especially for large organizations, with one stating, “It’s perfect for complex health systems, but can be difficult to grasp.”

Some users, however, expressed concerns about the platform’s usability, with one mentioning, “Cerner is efficient, but it can be overwhelming for new users, and the interface isn’t as intuitive.”

Final Decision: Which EMR Aligns With Your Practice Goals?

When choosing between athenahealth vs. Cerner, it's crucial to consider the specific needs and goals of your practice. athenahealth excels in providing a user-friendly, flexible platform ideal for small to mid-sized ambulatory practices. Whereas, Cerner is designed for larger, complex healthcare networks, offering robust interoperability and data management features.

Your decision should hinge on factors like practice size, workflow complexity, and integration requirements. Ultimately, selecting the EMR that aligns with your practice's long-term goals will enhance both patient care and operational efficiency.