Common Challenges in Custom EHR Development and How to Overcome Them

META-11-1024x538 Common Challenges in Custom EHR Development and How to Overcome Them

As of 2021, approximately 96 percent of all non-federal acute care hospitals and nearly 78 percent, which implies 4 in 5 office-based physicians, have adopted a certified EHR system.

Making the switch to electronic health records (EHRs) has become more popular due to their effectiveness in improving patient care, reducing errors, and streamlining workflows.

However, adopting and fully embracing custom EHR systems comes with its fair share of challenges, including staff training, concerns about data security, interoperability, and migration issues.

Key Challenges in Custom EHR Development

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1. Cost and Time

The cost of custom EHR development depends on various factors, such as the complexity of the features, the size of the healthcare facility, and the technology stack chosen. You’d need to consider expenses for software development, infrastructure, testing, and ongoing maintenance. It’s essential to allocate a substantial budget to ensure a robust and secure system.

In addition to that, developing a custom EHR system is a time-consuming process. It involves thorough planning, development, testing, and implementation phases. Depending on the complexity, it can take several months to even a few years. It’s crucial to factor in the time required for regulatory compliance and user training.


Phased implementation: One strategy is phased implementation. Instead of developing the entire EHR system at once, break it down into manageable phases. This allows you to prioritize essential features, control costs, and start using the system sooner. It also helps in gathering feedback for continuous improvement.

Open-source solutions: There are reliable open-source platforms for database management, security, and interoperability. This can significantly reduce development costs and speed up the process by utilizing existing solutions.

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2. Technical Expertise

One of the primary challenges in custom EHR development is the need for skilled developers and healthcare IT professionals. Health data is sensitive and requires a deep understanding of healthcare workflows and compliance standards. You’ll need experts who can design secure, scalable, and user-friendly systems.


Experienced vendors: Partner with experienced vendors who specialize in healthcare IT. They often have a team of experts with a proven track record in EHR development. They have pre-built modules and a wealth of knowledge to guide EHR development.

3. Interoperability

Seamless data exchange is crucial for effective EHR systems. One challenge is the diverse range of systems in healthcare. Ensuring your EHR can seamlessly communicate with other systems like lab databases and billing and even across different healthcare providers is a big task.


Industry Standards and APIs: Adhering to standards and using common data formats and protocols, like HL7 FHIR or openEHR, ensures interoperability. No more translators needed between different systems.

Moreover, developing robust APIs based on industry standards allows for a standardized way to access and exchange data. It’s like having a universal translator that ensures smooth communication between different systems.

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4. Data Security and Privacy

Data security is non-negotiable in healthcare. It’s not just a matter of reputation but also legal and ethical obligations. One major challenge is the sheer volume and complexity of data stored in an EHR, including medical history, diagnoses, prescriptions, and more- all highly personal and confidential.


Implementing data encryption: Data encryption is essential to safeguard patient information during storage and transmission. It adds an extra layer of protection against unauthorized access.

Access controls: Role-Based Access Control (RBAC) are critical for restricting access based on the user’s role or responsibilities. It minimizes the risk of unauthorized personnel accessing sensitive data.

Regulatory Compliance: Following HIPAA guidelines ensures that you’re meeting the legal standards for protecting patient privacy. You need to make sure your EHR system aligns with HIPAA regulations to avoid any legal issues down the line.

5. Workflow Disruption

Healthcare providers are accustomed to a certain flow of patient data, documentation processes, and communication methods within their current system. Introducing a custom EHR might require them to adapt to new interfaces, data entry procedures, and interaction patterns. This transition can lead to temporary inefficiencies and a learning curve, potentially slowing down productivity.


Involve end-users – To mitigate these challenges, it is crucial to involve end-users, such as doctors, nurses, and administrative staff, in the development process. Soliciting their input and understanding their specific workflow requirements can help tailor the EHR system to align with existing practices. This not only enhances user acceptance but also ensures that the system is designed to facilitate rather than hinder daily tasks.

6. Vendor Management

Vendor management in custom EHR development is crucial, and it comes with its own set of challenges. Imagine this: You have a specific vision, but the vendor interprets it differently. Miscommunication leads to wasted time, frustration, and potentially costly rework. In addition to that, keeping the project on track requires well-defined milestones with clear deadlines. But sometimes, those deadlines get missed, or worse, they’re not even clearly defined!

Moreover, Unforeseen costs, unclear intellectual property rights, and inadequate warranty clauses can create future headaches.


Clear Communication: You need a crystal-clear communication channels, regular meetings, and detailed documentation to ensure you and vendor are all on the same page.

Defined Milestones: You need a concrete project plan with achievable milestones and a mechanism to track progress and address any delays proactively.

Contract Negotiation: You need to involve legal counsel, thoroughly understand the contract terms, and negotiate for fair pricing and clear expectations on both sides.

Overcoming the Challenges in Custom EHR Development

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Thorough Planning and Needs Assessment:

First off, you need to emphasize the importance of defining our requirements, budget, and timeline right from the start. To conduct a comprehensive needs assessment, you need to understand the specific requirements of your users, healthcare providers, and other stakeholders. This will help you tailor the EHR to meet everyone’s needs.

In addition to that, consider scalability and flexibility of your EHR system. Your EHR system should be able to grow and adapt as the needs of the healthcare facility evolve.

Agile Development Methodology:

Agile seems like a solid approach for EHR development. One key aspect is the iterative development approach. Instead of building the entire EHR in one go, we break it down into manageable “sprints” focusing on specific features. Each sprint delivers a working piece, reducing complexity and showcasing progress. This way, as the regulations or needs evolve, you can easily adjust the features of the next sprint.

Throughout each sprint, you need to involve other stakeholders in testing and providing feedback. This ensures the EHR aligns with your vision and addresses actual user needs.

Moreover, frequent testing catches issues early, preventing costly rework later. We fix them within the sprint, maintaining high quality and reducing delays.

User-Centric Design:

User-Centric Design is crucial in custom EHR development. First off, stress the importance of involving end-users right from the start. Their insights are invaluable in understanding the workflow and functionalities needed.

In addition to that, regular user testing sessions can catch issues that might be overlooked. And don’t forget to actively seek and incorporate user feedback. It ensures the final product meets their needs and expectations.

Data Migration and Integration:

Migrating data from legacy systems can be complex due to differences in data structures and formats. One way to tackle this is by partnering with data migration experts. They have the expertise to navigate these challenges and ensure a smooth transition.

Furthermore, use standardized data formats for communication between systems. This helps in creating a common language for data exchange. It’s also essential to identify APIs and middleware that can facilitate integration without disrupting existing operations.

Ongoing Support and Maintenance:

Ongoing support and maintenance are vital because once you launch the EHR system, it becomes an integral part of your healthcare operations. You need to ensure its continuous functionality, fix any bugs or issues that might arise, and adapt it to changes in your processes or regulatory requirements.

Look for EHR vendors that offer 24/7 customer support and have a track record of quick response times. This way, if any issues pop up, we can get them addressed promptly to avoid disruptions in our healthcare services.


In conclusion, navigating the complexities of custom Electronic Health Record (EHR) development requires a strategic approach to address challenges such as interoperability, user adoption, data security, integration, regulatory compliance, scalability, resource constraints, user experience design, and change management.

Overcoming these hurdles involves adopting industry standards, robust security measures, effective training programs, and agile development methodologies. Thinkitive’s expertise in custom EHR software development stands as a testament to our commitment to revolutionizing healthcare through innovative, tailored solutions that enhance care quality and operational efficiency.

Frequently Asked Questions

1. Is custom EHR development right for my organization?

Custom EHR development may be right for your organization if you require tailored features, workflows, and integration. Assess your unique needs, budget, and timeline before deciding on a customized electronic health records solution.

2. What are the typical costs involved in custom EHR development?

Custom EHR development costs vary but typically include analysis, design, development, testing, deployment, and ongoing maintenance. Expenses depend on features, complexity, regulatory compliance, and integration requirements, ranging from thousands to millions of dollars.

3. How long does custom EHR development take?

Custom EHR development time varies based on complexity, features, and team efficiency. It typically takes several months to a year or more, with factors like design, testing, and implementation influencing the timeline.

4. How can I ensure data security and privacy with a custom EHR?

Implement strong encryption protocols, strict access controls, regular security audits, and compliance with relevant data protection regulations. Educate users on privacy practices, conduct regular training, and stay informed about evolving security threats to maintain a secure custom Electronic Health Record (EHR) system

5. What happens to my existing data during the transition?

During the transition, your existing data is typically migrated or transferred to the new system. It is important to ensure a seamless and secure process to avoid data loss or corruption.

6. How can I minimize workflow disruptions during implementation?

Plan thoroughly, communicate clearly, and involve key stakeholders from the start. Prioritize gradual implementation, provide training, and anticipate potential challenges. Regularly assess progress, address issues promptly, and adapt strategies as needed for seamless workflow integration.

7. What ongoing support and maintenance are available after custom EHR development?

Post-custom EHR development, ongoing support includes bug fixes, updates, security patches, and system enhancements. Maintenance ensures system reliability, compliance, and adaptation to evolving healthcare requirements, fostering a seamless user experience.

Ganesh Varahade

Founder & CEO of Thinkitive Technologies.

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