Diagnosis Coding and Sequencing FAQ

How important are the final diagnoses?

Very important. And notice the emphasis on diagnoses. The final diagnoses should reflect how difficult the case was, meaning the complexity of all the medical decision making including laboratory tests, EKG’s, x-rays, CT’s and treatment that was medically necessary. Since most claims are transmitted electronically, the quality of your final diagnoses may determine whether a claim is paid accurately or not.

A common problem is forgetting to list all relevant diagnoses. Take for example, a patient who passed out, hurt their head and suffered a laceration. All of the tests listed above may have been medically indicated. Listing “scalp laceration” as the only diagnosis wouldn’t begin to accurately reflect all the thought process involved assessing a patient who also had syncope and a head injury. Frequently multiple diagnoses are required.

When a patient has multiple diagnoses, which should be listed first?

If multiple medical problems were addressed and multiple diagnosis are needed to reflect the complexity of the care delivered, list the most important or serious condition the patient was treated for first.

For example, a patient may present with leg pain, but upon evaluation be found to have bilateral pedal edema secondary to new onset congestive heart failure requiring admission for further evaluation and treatment. Although the chief complaint may have been leg pain, the diagnosis of new onset CHF is more serious and would be listed as the first diagnosis. Whenever a patient requires admission to the hospital, the first diagnosis should clearly indicate the primary reason for admission.

A chronic condition requiring evaluation, treatment or factors into your decision-making process when determining management options should also be listed as a diagnosis. These are often referred to as co-morbidities. For example: a patient may present with cellulitis, but is found to have uncontrolled diabetes or hypertension during their visit, It would be appropriate to list the uncontrolled diabetes and hypertension as diagnoses.

ICD-10-CM Official Guidelines require some conditions and co-morbidities to be coded together. For example, a patient with chronic kidney disease (CKD) who is also hypertensive should always have hypertensive chronic kidney disease coded (I12.-I13), followed by the CKD stage (N18.-). A patient with diabetic foot ulcer would require multiple diagnosis codes describing the type of diabetes with foot ulcer (E11-.621), along with the laterality, specific foot location, and stage of the non-pressure foot ulcer (L97.-).

If a patient has multiple fractures, list the most severe fracture as the primary diagnosis.

If a patient has multiple burns of varying degrees or thickness, list the most severe burn first. Generally, 3rd degree burns should be listed before 2nd degree burns, which are listed before 1st degree/superficial burns. Additional codes should be assigned for the percentage of TBSA of the burn and the percentage involving third degree burns.

Can symptoms be used as the diagnosis?

The final diagnosis should always be as specific as possible. However, if at the end of an encounter, no clear diagnosis can be established, it is acceptable to code sign(s) and/or symptom(s) instead of a diagnosis. For example, a patient may present with abdominal pain and after careful evaluation no definitive cause such as gastritis, cholecystitis, pancreatitis, or bowel obstruction is identified. “Abdominal pain” would be an acceptable diagnosis. Note that for accurate ICD-10 code assignment, it is important to specify the location of the pain such as epigastric, RUQ, RLQ, etc.

Signs or symptoms that are routinely associated with a disease process do not need be listed separately. For example, a patient who presents with chest pain and is found to have an NSTEMI should be coded as an NSTEMI. There is no need to list the symptom of chest pain as a diagnosis.

Can I use “R/O” if I’m not sure of the final diagnosis?

The short answer is no. Medicare's Evaluation and Management Guidelines state although your differential diagnoses may include “possible,” “probable,” or “rule out” diagnoses to reflect the complexity of your medical decision making, ICD 10 coding rules state you cannot use R/O, probable, suspected, possible, etc. as diagnosis codes. Instead, the final diagnosis should reflect the highest degree of certainty known during the ED visit. For example, if appropriate cardiac patients may be diagnosed with STEMI, NSTEMI, unstable angina, or ACS. If a patient has chest pain of uncertain etiology, it should be classified as to the type of chest pain (chest wall, precordial, atypical, etc.)

Please note inpatient hospital coding rules can differ from outpatient coding.

How do I code SIRS and sepsis given qSOFA and the new sepsis definitions proposed in the Sepsis 3 article?

Sepsis 3 strives to change how we approach septic patients clinically, but by itself does NOT change diagnosis coding at this time. ICD-10 is published by the World Health Organization. In the United States, the National Center for Health Statistics, which is part of the CDC, is responsible for adapting it to use in America. Any modifications go through a thorough evaluation by the WHO & CDC to ensure clinical accuracy and utility before being adopted. Sepsis 3 made recommendations for code changes, but until the code changes are reviewed, accepted, and published in ICD-10, providers and payers should use the existing definitions.

Here is official advice from Coding Clinic, Third Quarter, 20161.

Question: We have seen the recently issued consensus definitions for sepsis and septic shock. How and when will this affect the coding of sepsis and septic shock for ICD-10-CM? Will the Cooperating Parties be modifying the coding guidelines because of the new clinical definitions for sepsis?

Answer: The coding guidelines are based on the ICD-10-CM classification as it exists today. Continue to code sepsis, severe sepsis and septic shock using the most current version of the ICD-10-CM classification and the ICD-10-CM Official Guidelines for Coding and Reporting. Code assignment is based on provider documentation (regardless of the clinical criteria the provider used to arrive at that diagnosis. 

  1. Copyright 1984-2017, American Hospital Association ("AHA"), Chicago, Illinois.

Please see the list of references in FAQ 10 for more information on ICD 10 coding.

Here are the four basic choices you currently have when coding SIRS and Sepsis conditions:

SIRS: Refers to signs and symptoms associated with a systemic inflammatory response. While Sepsis 3 uses the term “SIRS” for a patient with ≥ 2 criteria, in ICD-10-CM, SIRS refers to non-infectious conditions such as heatstroke, injury or trauma. Coders will need to specify if it is associated with organ dysfunction such as kidney failure, liver failure, or encephalopathy (R65.11) or not (R65.10). The underlying condition (heat stroke, trauma, etc.) should be listed first, followed by the appropriate code for SIRS (R65.1x) and then any associated conditions. If a patient has SIRS related to infection, use the diagnosis of sepsis or severe sepsis as discussed below.

SEPSIS: Refers to patients with a systemic infection, without organ dysfunction (A41).

If identifiable, code the underlying systemic infection. If at the time of your encounter, the specific organism is not identified, one may code for Sepsis, unspecified organism (A41.9). Sepsis due to a procedural complication, Infection following a procedure (T81.4-) or following incomplete spontaneous abortion (O03.37) should be coded first, followed by the specific infection. Remember, there is no code for a diagnosis of “urosepsis”. Newborn sepsis has its own unique code (P36). Note that “bacteremia” (R78.81) (a positive blood culture without other findings) is not synonymous with sepsis.

SEVERE SEPSIS: Refers to patients with a systemic infection, with organ dysfunction such as kidney failure, liver failure, or encephalopathy but without septic shock (R65.20). Severe sepsis requires at least three codes, and severe sepsis is never the primary code. The first code is for the underlying infection followed by the subcategory Severe sepsis without septic shock (R65.20). The provider can still use the code for Sepsis, unspecified organism (A41.9) as the first code at the time of presentation if unable to identify the source. Use additional codes such as Acute kidney failure (N17.-) or Septic encephalopathy (G93.41) to specify organ dysfunction.

SEPTIC SHOCK: Refers to patients with a systemic infection, with organ dysfunction and shock (R65.21). When diagnosing a patient with septic shock, at least three codes are required just as with severe sepsis. Septic shock is never a primary code.

Urosepsis: There isn’t a unique ICD-10-CM code for this condition. If the patient is septic without organ dysfunction then list Sepsis, unspecified organism (A41.9) as the principal diagnosis and Urinary tract infection, site not specified (N39.0) as contributing. If the patient has organ dysfunction, e.g. acute kidney failure, list Sepsis, unspecified organism (A41.9) as the principal diagnosis, Severe sepsis (R65.2-), Acute kidney failure (N17.-), and Urinary tract infection, site not specified (N39.0) are listed as contributing diagnoses.

ACEP Quality Improvement & Safety Section Commentary

Sepsis 3 article:

How do I code for a patient who is unresponsive since there is no ICD-10 code?

Best practice would be to list the medical condition that is causing the patient to be unresponsive. Since there is no code for “Unresponsive”, it would be better to list “Altered mental state”, “Unconscious”, “Coma”, or “Stupor” if medically appropriate. There are also codes for transient alteration of awareness (R40.4) and somnolence (R40.0).

The Glasgow Coma Scale (R40.2-) can be coded in conjunction with traumatic brain injury codes acute cerebrovascular disease or sequelae of cerebrovascular disease codes. These codes are primarily for use by trauma registries, but they may be used in any setting where this information is collected. The coma scale may also be used to assess the status of the central nervous system for other non-trauma conditions. The coma scale codes should be sequenced after the diagnosis code(s). Three codes, one from each subcategory, are needed to complete the scale. The 7th character indicates when the scale was recorded. The 7th character should match for all three codes. There is a GCS code set designated “at arrival to the Emergency Department.”

ICD-10-CM also includes a code set for NIH Stroke Scale 0-42 (R29.7- -). The score may be used in conjunction with acute stroke codes I63 to identify the patient’s neurological status and the severity of the stroke. These codes should be sequenced after the acute stroke diagnosis code(s).

How do I code for HIV and illnesses associated with HIV?

Patients known to have HIV or AIDS should generally have this listed as a co-morbid condition as it adds complexity to the medical decision making. Use additional codes for manifestations of HIV infection, if present.  Z21, Asymptomatic human immunodeficiency virus [HIV] infection status is to be applied when the patient without any documentation of symptoms is listed as being “HIV positive,” “known HIV,” “HIV test positive,” or similar terminology.  Patients with any known prior diagnosis of an HIV-related illness should be coded to B20. Once a patient has developed an HIV-related illness, the patient should always be assigned code B20 on every subsequent admission/encounter. Patients previously diagnosed with any HIV illness (B20) should never be assigned to R75 or Z21, Asymptomatic human immunodeficiency virus [HIV] infection status.

For a patient who is admitted, do the Emergency Department diagnoses and the hospital discharge diagnoses need to match?

Not necessarily. The Emergency Department diagnosis is based upon the clinical information available and should always be as specific as possible. The hospital discharge diagnoses may be the same, different, and may include additional findings. As discussed in FAQ 4, Emergency physicians may not code “rule out” diagnoses, coding guidelines for inconclusive diagnoses (probable, suspected, rule out, etc.) were developed for inpatient reporting and do not apply to outpatients. 

Does the final diagnosis affect payment?

Yes and no. Coding convention states that you don’t need a “final” diagnosis but that the diagnosis is to the level of clinical certainty for the encounter. The diagnosis code(s) help support medical necessity for the encounter. The level of service a physician gets paid should be determined by the Nature of the Presenting Complaint and the Complexity of the Medical Decision Making performed.

However, occasionally payers violate coding convention and use the final diagnosis to determine payment. Such a methodology ignores the cognitive work performed by physicians which defines the Complexity of Medical Decision Making. A patient may present with several symptoms, require a complex work-up, but be discharged with a non-life-threatening diagnosis. For example, a patient with a cough, tachycardia, and chest pain may require extensive testing such as complete blood count, basic metabolic panel, troponin, EKG, chest x-ray, and CT of the chest. However, the final diagnosis might be bronchitis which could lead a payer to wrongly deny the claim or down-code the Evaluation & Management level of service.

Best practice is to make sure the final diagnoses reflect all the issues addressed during the ED encounter, how complex the Medical Decision Making was, and the testing needed. In the example given above, in addition to diagnosing bronchitis it would likely be helpful to list tachycardia and chest pain to indicate why such an extensive work-up was performed.

Where can I learn more about ICD-10-CM?

National Center for Healthcare Statistics ICD-10-CM 

Official ICD-10 Guidelines

National Center for Healthcare Statistics ICD-10-CM
Official ICD-10 Guidelines

For questions about Claims Processing and Payment or Local Coverage Determinations:

Contact your Medicare Administrative Contractor (MAC) for guidance. See the list of MACs

Additional resources are located on the ACEP website:

ICD-10-CM and the Emergency Physician

ICD-10-CM For the Busy Emergency Physician

Updated March 2022


The American College of Emergency Physicians (ACEP) has developed the Reimbursement & Coding FAQs and Pearls for informational purposes only.   The FAQs and Pearls have been developed by sources knowledgeable in their fields, reviewed by a committee, and are intended to describe current coding practice. However, ACEP cannot guarantee that the information contained in the FAQs and Pearls is in every respect accurate, complete, or up to date.

The FAQs and Pearls are provided "as is" without warranty of any kind, either express or implied, including but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Payment policies can vary from payer to payer. ACEP, its committee members, authors or editors assume no responsibility for, and expressly disclaim liability for, damages of any kind arising out of or relating to any use, non-use, interpretation of, or reliance on information contained or not contained in the FAQs and Pearls. In no event shall ACEP be liable for direct, indirect, special, incidental, or consequential damages arising out of the use of such information or material. Specific coding or payment related issues should be directed to the payer.

For information about this FAQ/Pearl, or to provide feedback, please contact David A. McKenzie, ACEP Reimbursement Director at (469) 499-0133 or

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