Revenue Cycle Insider

Find out how to navigate these complicated coding situations correctly.

Selecting the principal diagnosis for inpatients who have complicated and evolving conditions can be very tricky. If you have accurate documentation to work with, then you can rely on the ICD-10-CM coding conventions to make sure you’re choosing the true principal diagnosis, in every sense of the term.

Heather Greene, MBA, RHIA, CDEI, CIC, RCMS, CDIP, CPC, CPMA, CDEO, CRC, shared her expertise on selecting principal diagnoses during her presentation “The Principles of the Principal Diagnosis” at AAPC’s 2025 HEALTHCON, including the following scenarios.

Try your hand at these scenarios detailing patients with multiple diagnoses, and see whether you can figure out what to code first.

Case 1: COVID-19, Sepsis, or Pneumonia?

A 69-year-old patient is admitted for hypotension and change in mental status. They were seen in the emergency department (ED) and notable vitals included hypotension, fever, and tachypnea. Bloodwork revealed hypernatremia, hyperkalemia, elevated chloride, low bicarb, acute kidney injury (AKI), hyperglycemia, acute on chronic anemia, albuminemia, CK/Troponin elevated. Patient positive for COVID-19 and strep in urine. A chest X-ray marked interval worsening of bilateral lung opacities, compatible with multifocal pneumonia and/or pulmonary edema. The physician lists these diagnoses: COVID-19, sepsis, and possible concurrent pneumonia.

What would be the principal diagnosis?

“For sepsis, there are guidelines, and every time I code sepsis, I go back and read it. As an auditor, I’ve coded a lot of sepsis and so I read it every time,” Greene said. “You have to code the systemic condition first, right?

“If severe sepsis meets the definition of the principal diagnosis, you code the systemic infection first and severe sepsis second,” Greene said. Remember, the ICD-10-CM Coding Guidelines Chapter 1: Certain Infectious and Parasitic Diseases (A00-B99) U07.1, U09.9, say that neither severe sepsis (or associated organ dysfunction) nor septic shock can be coded as a principal diagnosis.

Though this patient is experiencing several infections simultaneously, Greene said that you have to follow the sequencing rules, which means knowing that you can’t code pneumonia as the principal diagnosis because it’s a localized infection. In this situation, there’s also possibly a localized infection in the urinary tract, suggested by the presence of strep bacteria in the urine, as well as a diagnosis of COVID-19.

If you’re considering COVID-19 as the principal diagnosis, look to the guidelines. When you look at the coding guidelines for COVID-19, the Sequencing of codes instructions say: “When COVID-19 meets the definition of principal diagnosis, code U07.1, COVID-19, should be sequenced first, followed by the appropriate codes for associated manifestations, except when another guideline requires that certain codes be sequenced first, such as obstetrics, sepsis, or transplant conditions.”

When figuring out the principal diagnosis, go back to what brought the patient to the hospital, Greene explained. In this case, the patient came to the hospital for hypotension and a change in mental status, which the physician attributed, in part, to sepsis.

Case 2: Acute Kidney Failure, Chronic Fatigue, or Other?

This patient is an 82-year-old transferring to a skilled nursing facility (SNF) whose history includes cancer and transplant. Their physician made a diagnosis of renal failure — but once you see mention of transplant, you should consult the guidelines and consider “complication,” Greene said.

Looking at the diagnoses, you have the options of coding acute kidney failure, chronic fatigue, or something else entirely. If you reference Chapter 14: Diseases of the Genitourinary System (N00-N99), you’ll see a note to “See section I.C.19.g for information on coding complications of a kidney transplant.”

Following these instructions, you’ll find this guidance: “… Code T86.1- should be assigned for documented complications of a kidney transplant, such as transplant failure or rejection or other transplant complication … Conditions that affect the function the function of the transplanted kidney, other than [chronic kidney disease] CKD, should be assigned a code from subcategory T86.1, Complications of transplanted organ, Kidney, and a secondary code that identifies the complication.”

Accordingly, the principal diagnosis in this case would not be acute kidney failure or chronic fatigue, but T86.1 (Complications of kidney transplant) and then secondary code T86.12 (Kidney transplant failure) to identify the complication.

Rachel Dorrell, MA, MS, CPC-A, CPPM, Development Editor, AAPC