Diagnosis Coding and Sequencing FAQ

1. Where do the coding guidelines come from?

The International Classification of Diseases (ICD) 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 US clinical modifications (ICD-10-CM). US modifications go through a thorough evaluation by the CDC and CMS to ensure clinical accuracy and utility before being adopted. Modifications must be within the context of the WHO version. ICD-10-CM guidelines and codes are part of the HIPAA transaction code set that all payers are required to follow for electronic healthcare transactions.

AHA Coding Clinic® for ICD-10-CM/PCS, published quarterly by The Central Office of the American Hospital Association, serves as the official source for coding information (Federal Register, Vol. 74, No. 165, Thursday, August 27, 2009). Responses for publication are reviewed by the Editorial Advisory Board which consists of physician representatives, facility coders and the Cooperating Parties (AHA, HCHS, CDC and AHIMA).

2. How important is the principal diagnosis?

It is key. The principal diagnosis along with contributing/secondary diagnoses reflect the risk or morbidity and mortality. They support resource utilization and reflect the complexity of 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 accuracy of your diagnoses may determine whether a claim is paid appropriately or not.

All  relevant diagnoses should be assigned which contribute to the evaluation and management of the patient. Take for example, a patient who passed out, hit 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.

ICD-10-CM Official Guidelines for Coding state that a diagnosis is based on “the highest degree of [clinical] certainty for that encounter/visit, such as symptoms, signs, abnormal test results, or other reason for the visit”. You do not need a "final" diagnosis.

3. 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.

Chronic condition(s) requiring evaluation, treatment or which factor into your decision-making process when determining management options should also be listed as secondary diagnoses. These are often referred to as co-morbidities. For example: a patient may present with cellulitis and is found to have uncontrolled diabetes and hypertension during their visit.  It would be appropriate to list the Type 2 diabetes with hyperglycemia and hypertension as additional diagnoses.

ICD-10-CM Official Guidelines has a coding convention where certain conditions that have both an underlying etiology and co-morbidities or multiple body system manifestations due to the underlying etiology requires the underlying condition be sequenced first, if applicable, followed by the manifestation. In the ICD-10-CM tabular wherever such a combination exists, there is a “use additional code” note at the etiology code, and a “code first” note at the manifestation code. For example, a “code first” notation is found at chronic kidney disease (CKD) (N18) directs you to code first related disorders such as hypertensive chronic kidney disease (I12.-, I13.-). In the case of “use additional code”. under Sickle-cell disorders (D57) you would find use additional code for any associated such as fever in chronic pre-existing conditions (R50.81). The physician is not limited to the “code first” and “use additional code” examples listed in the tabular, but may list other diagnosis codes, that in their opinion, is related to the etiology or manifestation.

If a patient has multiple fractures, list the most severe fracture as the primary diagnosis.  By the ICD-10-CM Official Guidelines, open fractures are coded primary to closed fractures.  A fracture not specified as non-displaced is coded to displaced.

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.

4. Can symptoms be used as the diagnosis?

The principal 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) for the clinical impression. 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, periumbilical or generalized, etc.

Signs or symptoms that are routinely associated with a disease process are not 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. Similarly, cough is implicit in bronchitis. Similarly, vomiting and diarrhea are considered inherent in gastroenteritis and would not be coded separately.

5. Can I code “R/O” if I’m not sure of the principal diagnosis?

While your differential diagnoses may include “possible,” “probable,”, “rule out” or “consistent with” diagnoses to reflect the complexity of your medical decision making, ICD 10 coding rules for outpatient services state you cannot use these “indeterminant terms” as diagnosis codes. Instead, the principal diagnosis should reflect the highest degree of certainty known during the ED visit. If a patient has chest pain of uncertain etiology, it should be classified as to the type of chest pain (chest wall, precordial, atypical, or unspecified, etc.). However, if the physician lists a diagnosis as definitive, even if noted with an indeterminant term in the MDM, it is codes for that condition. For example, the physician may note “lab findings consistent with dehydration”, it would be coded as definitive if listed as a discharge diagnosis.

Inpatient hospital coding rules differ from outpatient and professional fee coding. Inpatient, uncertain diagnoses which are not ruled out prior to discharge or demise get coded. Best practice is to combine uncertain diagnoses with signs or symptoms, explaining what the provider is thinking as well as giving everyone a compliant codable diagnosis (e.g., Epigastric pain, rule out acute gastric ulcer).

6. How do I code SIRS and sepsis given the 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. Sepsis-3 made recommendations for code changes, but until the code changes are reviewed, accepted, and published in ICD-10-CM, providers and payers need to use the existing definitions. Sepsis-3, however, recommends the use of the current ICD-10-CM codes that are listed under “severe sepsis”. The physician needs to be aware of these technical differences in their documentation. They should not use the term “sepsis” when the patient meets the criteria for “severe sepsis”.

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. In ICD-10-CM the term “SIRS” refers to non-infectious conditions such as heatstroke, injury, or trauma. Documentation will need to specify if this condition is associated with organ dysfunction such as kidney failure, liver failure, or encephalopathy (R65.11) or without organ dysfunction (R65.10). The underlying condition (heat stroke, trauma, etc.) should be listed first, followed by the appropriate code for SIRS (R65.1-) and then any associated conditions. If a patient has a systemic inflammatory response related to infection, use the diagnosis of sepsis or severe sepsis as discussed below.
  • SEPSIS: In ICD-10-CM, the term “sepsis” is used to identify the organism that is the cause of the systemic infection. The code A41.9 (Sepsis, unspecified organism) is used if the type of infection or causal organism is not further specified. In addition, there are codes for specific conditions such as puerperal sepsis (O85.-), newborn sepsis (P36.-), and sepsis following a procedure (T81.44XA). Remember, there is no code for a diagnosis of “urosepsis” (see below). Note that “bacteremia” (R78.81) (a positive blood culture without other findings) is not synonymous with sepsis.
  • SEVERE SEPSIS: This term refers to patients with a systemic infection and with organ dysfunction such as kidney failure, liver failure, or encephalopathy but without septic shock (R65.20). While not the term recommended by Sepsis-3, it is the recommended ICD-10-CM code for patients meeting the SOFA criteria for sepsis. The first code is for the underlying sepsis followed by the subcategory severe sepsis without septic shock (R65.20). The code for severe sepsis is never the primary code. The provider can use the code for "Sepsis, unspecified organism” (A41.9) as the first code at the time of presentation if unable to identify a more specific etiology. 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). This is the Sepsis-3 recommended ICD-10-CM code for patients meeting the SOFA criteria for septic shock. Coding is sequenced in the same manner as severe sepsis, with the cause of the sepsis listed first, septic shock secondarily and additional codes to identify organ dysfunction. 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, as the principal diagnosis and urinary tract infection or acute pyelonephritis as contributing. If the patient has organ dysfunction, e.g., acute kidney failure, list Sepsis as the principal diagnosis, Severe sepsis (R65.2-), Acute kidney failure (N17.-), and Urinary tract infection are listed as contributing diagnoses.

7. 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”, use the code that best explains the patient’s presentation. This can range from “Encephalopathy” (including metabolic, toxic, hypertensive, other, and unspecified) to  “Altered mental state,” “Unconscious,” “Coma,” or “Stupor”.  There are also codes for transient alteration of awareness (R40.4) and somnolence (R40.0).

ICD-10-CM also includes a code sets for NIH Stroke Scale 0-42 (R29.7- -) and coma scale (R40.2-). The Stroke Scale 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). The coma scale is used with any associated traumatic brain injury and can indicate the time frame when performed, e.g., pre-hospital score, score on arrival to the ED.

8. 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 a 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.

9. 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 facility reporting and do not apply to outpatients.

10. Does the principal 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 principal 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 principal 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 principal 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.

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

National Center for Healthcare Statistics ICD-10-CM

Official ICD-10 Guidelines

2023 ICD-10-CM codes (indexes and tabular)

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 May 2023


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 from 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 Jessica Adams, ACEP Reimbursement Director, at (469) 499-0222 or

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