Urology Coding Dos and Don’ts: Guidelines for Best Practices

Billing and coding is one of the most important aspects of running a urology practice. But it can be confusing, especially for people who aren’t professional coders. We’ve taken the guesswork out of basic urology coding with these guidelines, so you and your practice can navigate the process with greater confidence.

Urology coding basics

Select the right code

There are three main categories to consider when performing CPT coding for urology: evaluation and management (E/M) codes, procedure codes, and add-on codes.

1. E/M codes: E/M stands for evaluation and management. These are used to bill for professional services, such as physician and nonphysician practitioner clinic visits, hospital visits, or consultations, most commonly found between 99202 and 99499.
2. Procedure codes: These codes are those used to bill for diagnostic and treatment services, most commonly found between 50010 and 58999.
3. Add-on codes: These codes identify procedures carried out in addition to the primary procedure. In the CPT manual, these are designated with the “+” symbol. These codes may be payable if reported with the appropriate primary procedure.

Knowing these general categories and where to find them can narrow the field considerably when selecting a code. 

Stay up-to-date on billing code changes

All CPT codes are updated annually, with changes incorporated into the CPT code set on January 1. Staying current with these updates is essential to support accurate billing and uninterrupted cash flow. CPT and related billing changes that could have a direct impact on your urology practice in 2026 include:

1. Expansion of setting for providers to bill HCPCS add-on code G2211 with home or residence E/M codes.
2. Extended Medicare telehealth flexibilities through December 31, 2027. 
3. Ten new, approach-specific biopsy codes and one add-on code replacing the former prostate biopsy code 55700.
4. Two new prostate surgery codes and the deletion of code 52647 for reporting laser coagulation of prostate.
5. Revisions to code 55866, which indicate that additional codes will fall under 55866. This descriptor is now included in codes 55868 and 55869.
6. Revisions to code 55705 so it now reads: Biopsy, prostate, any approach, nonimaging-guided.

Sweat the small stuff

For example, in cases involving a bladder cancer diagnosis, billing staff should check the procedure notes for the location from which the bladder tumor was removed. One common mistake is overusing C67.9, bladder cancer unspecified. Typically, an unspecified diagnosis should be used only when the information in the medical record is insufficient to assign a more specific code. It would be extremely rare that there would be no mention of the location of the tumor removal in the procedure notes, so your claim could come back rejected due to unspecified coding.

Examples of codes with more specificity:

• C67.0 Malignant neoplasm of trigone of bladder
• C67.1 Malignant neoplasm of dome of bladder
• C67.2 Malignant neoplasm of lateral wall of bladder
• C67.3 Malignant neoplasm of anterior wall of bladder
• C67.4 Malignant neoplasm of posterior wall of bladder
• C67.5 Malignant neoplasm of bladder neck
• C67.6 Malignant neoplasm of ureteric orifice
• C67.7 Malignant neoplasm of urachus
• C67.8 Malignant neoplasm of overlapping sites of bladder

The frustration and duplication of work from denials associated with unspecified codes can be avoided. Remember, coding must be supported with proper documentation, and code selection should take the documentation into account. Otherwise, you could run the risk of missing small but important details that could result in claim rejection. 

ICD-10-CM is updated annually on October 1. Practices that regularly check for these updates may save time when deciding if a selected code is an appropriate choice in terms of specificity for a given diagnosis.

Urology coding dos and don’ts for a smooth billing experience

Do have human eyes on code selection — always

EHR-suggested coding functions are meant to facilitate correct selection, not take the place of it. Therefore, the provider and billing and coding staff must always review the selected or suggested code for accuracy. 

Do train providers on proper documentation and coding procedures

It’s important for physicians to receive proper documentation and coding training on a regular basis since codes and their descriptions change annually. Providing care to a patient contains nuances that billing and coding staff are not trained to capture because they aren’t clinically trained. Providers should be involved in code selection and review. Using outdated or unlisted codes could affect reimbursement rates. Furthermore, missing new add-on codes or new levels of specificity that could have been appropriately billed could result in missed revenue opportunities.

Don’t undercode to avoid an audit

Undercoding is the practice of selecting codes that fail to capture all work performed. This most often happens simply due to oversight, but some practices do it because they think it will reduce the chance of an audit. Undercoding may result in lost revenue due to services not being reported, but it can also result in a skewed data pattern or inconsistent billing, which may be perceived by Medicare as a deviation compared to the billing of your peers. In those cases, undercoding itself may lead to an audit. Intentional undercoding can also be considered an impermissible inducement to patients if it results in lower patient financial responsibility. 

How ModMed handles coding

Our latest AI-Powered documentation tool, ModMed^® Scribe 2.0, transforms natural conversation into suggested visit notes, prescriptions, lab orders, and more, in seconds.

Additionally, when using our EMA^® EHR, you can use our specialty-specific plans created by practicing urologists that use structured data to pick up on MDM requirements based on American Medical Association guidance in order to make code suggestions. The code suggestion, including modifiers, is based on your documentation.

Protocols can include your commonly seen diagnoses, treatments, orders, and more into a single touch to help you speed up documentation, and EMA will suggest coding. EMA also provides a rationale explaining the factors for the code’s suggestion. For example, using a protocol for a visit to evaluate a prostate nodule may suggest an E/M code of 99212, then allow you to modify details, including nodule features and location.

It’s important to remember that the ultimate legal responsibility for documentation accuracy and coding lies with the provider, not the software. You need to have human eyes on the code selection and supporting documentation to ensure you’re covered in the event of an audit.

Within EMA, code suggestions and the underlying supporting data are easily editable. For example, selecting the status button to the right of the exam opens the Presenting Problem Complexity sub-window, allowing you to modify the Medical Decision Making factor without leaving the Virtual Exam Room (VER).

Let’s say the Risks of Complications were slightly more complex than usual. Documenting additional information in this area of the MDM may increase the level and could change the E/M code, depending on other factors you’ve documented during the visit. The chart note is your place to include the pertinent supporting documentation you need to justify the code to payers — all stored within EMA.

Remember that our software’s suggested codes are just that — suggestions. Before finalizing the visit, you must confirm that the selected code accurately reflects the medical documentation and that the services provided were medically reasonable and necessary.

Commonly seen cases in urology coding

Let’s say you’re seeing a patient for a possible vasectomy. Best medical practice is generally to perform an initial visit or consultation, then the procedure at a later date, giving the patient time at home to consider all the risks and benefits. That could be one E/M code (for the consultation) and one procedure code (for the vasectomy), billed separately on different dates of service.

But what happens when you need to bill more than one code category in a single visit? For example, when a patient presents with an abscess that requires immediate removal. An evaluation is performed and the provider decides the procedure must happen immediately to protect the health of the patient. How do you code these events appropriately?

EMA can recognize these situations based on the documentation, even if the provider indicates a separate evaluation was needed from the procedure itself. This can be accomplished with the Separate & Identifiable Plan under the Plan tab. This option can be used when an E/M code and procedure code must be billed out of medical necessity, and it suggests the appropriate modifier on the E/M code. It captures the information needed to justify multiple categories of services occurring in a single visit.

Useful coding functions in EMA for urologists

The Override Billing function can be accessed after a note is complete and before it is finalized. This function brings up the full MDM calculation for you to review and modify if needed. Additionally, you can bill by time from this option if you choose. Simply input the total time spent with the patient on that calendar day and select the associated activities you performed from a pregenerated list or by using free text, then select Bill by Time.

The ICD-10 Expert function helps decrease claim denials due to a lack of specificity, and it will automatically pop up when certain diagnoses are selected that often require a further layer of specificity modifier. For example, selecting “hematuria” in EMA will prompt the ICD-10 Expert to open, asking you what kind of hematuria the patient is experiencing and capturing code specificity. Claim denials slow down your accounts receivable and are a pain to reconcile. This function can help lead to cleaner claims moving forward.

EMA’s coding suggestions can also help providers and staff save time during the day.

2026 Medicare Physician Fee Schedule impact on urology

New for 2026, the Centers for Medicare & Medicaid Services (CMS introduced two separate conversion factors: one for advanced alternative payment model (APM) participants, and one for all others. The conversion factor for APMs will increase to $33.57, an increase of 3.77%, and the conversion factor for all others will increase to $33.40, an increase of 3.62%. CMS also adjusted the methodology for allocating indirect practice expenses, which is expected to decrease overall charges for urology in the facility setting by 10%, but increase payments by 5% in the office setting. 

There is also a 2.5% efficiency adjustment decrease in effect in 2026 for almost every service on the fee schedule, with the exception of time-based codes, services on the CMS telehealth list, and new codes for 2026. The financial impacts of these reimbursement changes on urology practices will vary based on practice type, payer type, mix of patients, and types of services provided, but overall, according to the AMA, these changes affect nearly 7,000 physician services and impact 91% of services provided by physicians. 

Want to learn more about how our software can help you keep up with ever-changing coding regulations and industry standards?

Reach out to our urology team today.

1 “What Is CPT^®?” AAPC.

2 “Medicare NCCI Add-On Code Edits.” Centers for Medicare & Medicaid Services. September 10, 2024.

3 “2026 ICD-10-CM Diagnosis Code C67.9: Malignant Neoplasm of Bladder, Unspecified.” ICD10Data.com.

4 Dowling, Renee. “Common Coding Problems, From Unbundling to Undercoding.” Medical Economics. February 27, 2023.

-This blog is intended for informational purposes only and does not constitute legal or medical advice. Please consult with your legal counsel and other qualified advisors to ensure compliance with applicable laws, regulations and standards.

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