Overview

Many EHR systems were designed for general practice, and then adapted for everyone else. This can be a challenge when running a fertility clinic, an oncology practice, or an orthopedic center, where documentation, order placement, and follow-up are completely different from that of a general practitioner. It no longer comes down to adoption. By 2024, 91% of U.S. office-based physicians were using a certified EHR, as reported by the Office of the National Coordinator for Health Information Technology. But the question is about fit – which is why an increasing number of specialty clinics are looking for a development partner to create one. Here's how to choose.

Why Off-the-Shelf EHRs Fall Short for Specialty Care

There is friction in the numbers. In 2024, the Journal of General Internal Medicine published a study based on the statistics for more than 200,000 doctors and found that physicians spent an average of 3.4 hours in the EHR (or around 58% of their clinical time), plus 1.2 hours out-of-hours each day. Just documenting takes roughly 2.3 hours for every 8 hours of scheduled patient appointments.

And that workload isn't shared equally. Indeed, the same study also found significant differences between specialties: 8.4 hours on average were spent by infectious disease specialists for every 8 hours of patient visits on EHR duties, compared with just 2.5 hours for anesthesiologists. A generic template that does well enough for one group actively hinders another.

Specialty clinics hit specific walls that general-purpose systems rarely anticipate:

If software is fighting against the workflow, people come up with hacks: spreadsheets, notes stuck everywhere, duplication of entries. And these hacks are the places where errors and lost revenue can be found.

What an EHR Development Partner Actually Does

Before evaluating vendors, define the scope of work since the term “EHR partner” can mean quite different things. Some vendors specialize in developing EHR systems from scratch, while others specialize in customizing certified platforms, implementing third-party modules, and maintaining and extending the software owned by you.

A capable provider of EHR software development services usually handles some mix of the following:

1. Discovery and workflow mapping. Meeting together with your medical professionals to define how the patient care flows in your practice, and then creating the system around that workflow.
2. Custom module development. Developing the domain-specific components such as templates for protocols and patient evaluations, scores, custom order sets, and patient-facing applications.
3. Integration. Integrating the EHR with lab information, picture archiving and communication systems, billing, pharmacy management systems, and patient portals.
4. Compliance engineering. Engineering the system for HIPAA compliance by implementing security measures, audit logging, and access control mechanisms.
5. Ongoing support. Software maintenance, upgrades, and customization.

That makes a difference, because in case one needs mostly the deep integration of the existing platform, the best product developer may not be the right partner. And vice versa. You need to find the partner whose strengths match your needs.

Deciding early on whether to fall on the build side or configure side of the equation is also critical. A complete build of a custom EHR gives you total control and the closest match for your workflow but at the greatest cost and timeline and requires ongoing maintenance of a certified system. Extending or configuring an existing certified platform is faster and cheaper, but comes with the restrictions of that platform. Specialty clinics tend to fall in between: keep the certified base system but contract out the specialty layer. Knowing where among these three options you lie transforms a vague “we need better software” into a concrete that vendors can bid on.

The Criteria That Separate a Strong Partner from a Risky One

With scope determined, evaluate potential partners based on criteria that will predict success in healthcare, not just generic software quality.

Healthcare domain experience. Making healthcare software is not the same as making retail software. Request relevant case studies, and check references who use their own clinics as similar to yours. Domain experience in your particular specialty (or a related specialty) reduces learning curve significantly and avoids the “we didn’t realize clinics work like that” surprises.

Regulatory fluency. Your partner needs to be able to discuss HIPAA compliance, the ONC Health IT Certification Program, and the provisions in the 21st Century Cures Act relating to information blocking. If certification is part of your reimbursement process, make sure that they've done it on previous software projects, not on yours.

Interoperability standards. Information has to flow, and there are industry-standard methods for doing so: HL7 and FHIR (Fast Healthcare Interoperability Resources). This is not window dressing. In 2023, 70% of U.S. hospitals conducted four-way interoperable exchange (transmitting, receiving, searching, and integrating information) at least sometimes, according to ONC statistics; only about 43% did so regularly. A partner that builds with FHIR from the beginning helps keep your clinic above that gap.

Security practices. Find out how they address encryption, access controls, breach response, and data hosting. The healthcare sector is one of the most vulnerable to data breaches and a weakly built project leaves you liable beyond its lifespan.

A realistic delivery model. What does their model look like? Iterative deployment with functional milestones, not a one-time launch a year away. You need to see and test the software as it evolves, so that problems become evident while they're easy to solve.

Questions to Ask Before You Sign

Not the high resolution pitch deck thing. It's about the short, concise speech. Provide to serious candidates:

• What do both the code and data look like at the end of the engagement?
• What will be the cost of the support/maintenance after launching and how will it be managed?
• What is your approach for downtime, backups and disaster recovery?
• Ever present a project that was HIPAA compliant, what steps did you take to make the project HIPAA compliant?
• How will we be moving our current patient data and how will we secure it during the move?
• What will you do if the project exceeds time and/or cost?

A general or defensive reaction is a big sign as to how things will go with the working relationship whether it's who will own the data, how they will support you after you've worked through it, etc.

Red Flags Worth Walking Away From

There are some red flags to be treated as deal breakers:

• No healthcare references. Basic software skills will not include knowledge about clinical processes.
• Silence on compliance. It should be addressed in case when HIPAA and certification are not mentioned by yourself.
• Lock-in by design. Proprietary format and lack of source code sharing guarantee that you can choose only one company.
• A firm quote with no discovery.  If there is no study of your workflow and a price is provided, it is likely that scope of work is not accurate.
• Overpromising on timeline. Quick implementation of medical software results in errors in both safety and billing.

The Bottom Line

Selecting your EHR development partner is a clinical choice as much as it is a technical one. The following three factors play a crucial role:

1. Fit over features. Vendor that understands workflow of your specialty is better choice than one with longer feature list.
2. Compliance and interoperability aren't negotiable.  Include them from the very beginning with standard such as FHIR.
3. Protect your exit. Have clear information about data ownership and code in your contract.

First thing you should do is to write down three workflows that irritate your team the most. Take this list to your first conversation with potential vendor and use their responses to problems rather than marketing materials for choosing candidates.