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Once you understand a few peculiarities, you'll be ready to code common diseases of the respiratory system.

Fam Pract Manag. 2014;21(6):17-22

Author disclosure: no relevant financial affiliations disclosed.

“Diseases of the Respiratory System” (J00-J99), perhaps more than any other chapter in ICD-10, leaves room for physicians to make a judgment call about how to code certain conditions. Before we get into the codes themselves, let's explore a few confounding factors:

1. Symptom vs. diagnosis. With the exception of streptococcal pharyngitis and tonsillitis, a specific infectious agent causing a disease is rarely identified at the time of the initial visit. ICD-10 allows you to report signs or symptoms (R00-R99) when you have not yet established or confirmed a related definitive diagnosis; however, sometimes what seems like a sign or symptom might actually be considered a diagnosis in ICD-10. Take “sore throat” for example. Code R07.0, “Pain in throat,” specifically excludes “sore throat (acute),” but J02.9, “Acute pharyngitis, unspecified,” specifically includes “sore throat (acute).” Therefore, it appears that ICD-10 considers “sore throat” to be a definitive diagnosis rather than a symptom.

2. Acute vs. acute recurrent. In ICD-9, codes were divided into “acute” and “chronic” conditions. In ICD-10, there is the additional classification of “acute recurrent.” In the absence of specific definitions, you must use your judgment to determine the time frame between episodes that would qualify a condition as “acute recurrent.” Your documentation will need to support whichever classification you use.

3. Inflammation vs. infection. Although the suffix “itis” references inflammation, the conditions pharyngitis, tonsillitis, sinusitis, etc., are all subcategories under “Acute upper respiratory infections” (J00-J06) in ICD-10. So, when you see an inflammation that is not from an infection, you need to look for a more specific code.

4. Multiple sites vs. the lower anatomic site. ICD-10 instructs that when a respiratory condition is documented as occurring in more than one site and there is not a specific code for that condition, it should be classified to the lower anatomic site. The example the ICD-10 book provides is tracheobronchitis being coded as bronchitis (J40).

5. Unspecified vs. lacking specific documentation. Although ICD-10 includes unspecified codes such as J06.9, “Acute upper respiratory infection, unspecified,” to avoid claim denials think carefully before using them. The use of unspecified codes is discouraged if you're using them because of a lack of clinical documentation.

6. Tobacco vs. no tobacco. ICD-10 requires that if tobacco is a factor in any illness, you must add the appropriate code from the F or Z series to identify current use, history of use, or exposure. (See “Tobacco use or exposure codes.”) Given the frequency of smoking as a causative agent in respiratory conditions, you'll want to keep these tobacco codes in mind.

Nicotine dependence
Chewing tobaccoF17.22*
Other tobacco productF17.29*
Tobacco use (problems related to lifestyle)Z72.0
Exposure to environmental tobacco smoke – occupationalZ57.31
Exposure to environmental tobacco smoke (second-hand smoke exposure and passive smoking)Z77.22
Personal history of nicotine dependenceZ87.891

Now that you are aware of these idiosyncrasies, which can affect both your documentation and your coding, let's navigate through the respiratory system.


This article contains several code lists and tables, which are available here for download as a single resource.

Acute nasopharyngitis

Ready for some good news? The common cold is still the common cold and has a simple, three-digit ICD-10 code: J00, “Acute nasopharyngitis.” ICD-10 even includes “common cold” in the description.


The ICD-10 codes for sinusitis align fairly well with those in ICD-9. Both sets include maxillary, frontal, ethmoidal, and sphenoidal. ICD-10 adds the option of pansinusitis. In ICD-9, pansinusitis fell under “Other”; however in ICD-10, “Other acute sinusitis” (J01.80) is for infections involving more than one sinus but not pansinusitis. Both ICD-9 and ICD-10 include a code for unspecified.

Each of the acute sinusitis codes requires a fifth digit that differentiates “acute” from “acute recurrent.” The chronic codes have only four digits. (See “Sinusitis codes.”)

If the cause of the sinusitis is known, add a code from B95-B97, “Bacterial and viral infectious agents,” to identify the infectious agent.

Acute sinusitisAcute recurrent sinusitisChronic sinusitis

Clinical scenario: A 62-year-old female presents to your office with classic symptoms of sinusitis. She has no known risk factors other than sharing a household with her husband who smokes in the residence. On examination, you are able to elicit tenderness over the maxillary sinuses only. You place her on a two-week course of oral antibiotics and assign code J01.00.

After completing the antibiotics, she returns with persistent symptoms. She is now tender over both the frontal sinuses as well as the maxillary sinuses. You prescribe a different antibiotic for a longer course and arrange to see her again in four weeks. The condition is not yet recurrent or chronic, so you assign code J01.80, “Other sinusitis, acute,” which is for infections involving more than one sinus. You also document the second-hand smoke exposure using Z77.22, “Contact with and exposure to environmental tobacco smoke.”

On her follow-up visit, her condition has completely resolved.

Three months later, she again presents with maxillary sinusitis. Because she has gone a significant period of time without signs or symptoms, you use the acute recurrent code J01.01.


The pharyngitis codes are also pretty straightforward. The condition can be acute or chronic and due to streptococcus, due to a known agent other than streptococcus, or unspecified. (See “Pharyngitis codes.”) Three additional causes of acute pharyngitis that may be identified in the primary care office are excluded from this category: gonococcus (A54.5), herpes (B00.2), and mononucleosis (B27.-). These codes are typically used for a follow-up visit after the results of previously ordered labs are available.

Streptococcal pharyngitisJ02.0
Acute pharyngitis due to other specified organismsJ02.8
Acute pharyngitis, unspecifiedJ02.9
Chronic nasopharyngitisJ31.1
Chronic pharyngitisJ31.2

Tonsils and adenoids

This group of codes, like the sinus codes, includes acute, acute recurrent, and chronic codes. It also includes a set of codes for non-infectious conditions. In a similar manner to ICD-9, there are separate codes for abscess and for hypertrophy. Adenoid vegetations had a stand-alone code in ICD-9, but this condition was merged into “Other chronic diseases of tonsils and adenoids” in ICD-10. (See “Tonsil and adenoid codes.”)

Adenoiditis, chronicJ35.02
Adenoids, hypertrophyJ35.2
Acute streptococcalJ03.00
Acute recurrent streptococcalJ03.01
Acute, due to other specified organismJ03.80
Acute recurrent, due to other specified organismJ03.81
Acute, unspecified
Acute recurrent, unspecifiedJ03.91
Peritonsillar abscessJ36
Tonsils, hypertrophyJ35.1
Tonsillitis and adenoiditis, chronicJ35.03
Tonsils and adenoids
Other chronic diseasesJ35.8
Chronic disease, unspecifiedJ35.9

Clinical scenario: A 4-year-old male is brought in to your office with an acute sore throat. A rapid strep test is positive, and you place him on an appropriate course of penicillin. You code the visit J03.00.

He presents two months later in the same manner with the same result. You again treat him but now use the recurrent code J03.01.

He has two additional episodes over the next four months.

At his 5-year-old preventive care examination, you note that he has significant enlargement of his tonsils and adenoids. You do not detect any sign of a current infection or abscess. You code the visit using Z00.121, “Encounter for routine child health examination with abnormal findings” (primary) and J35.3, “Hypertrophy of tonsils with hypertrophy of adenoids” (secondary).

Larynx, trachea, and epiglottis

These codes include acute (with or without obstruction) and chronic codes, but there are no acute recurrent codes. The unspecified codes do not differentiate between the larynx and trachea but use the term “Supraglottitis.” (See “Larynx, trachea, and epiglottis codes.”)

Note that while tracheitis and supraglottitis are divided into “with” and “without obstruction” by the use of a fifth digit, acute obstructive laryngitis (croup) has a stand-alone four-digit code, J05.0.

Hopefully, you will rarely see acute epiglottitis in the office, but be aware that there are codes for this condition without obstruction (J05.10) and with obstruction (J05.11).

There are separate codes for noninfectious conditions, such as those related to the vocal cords and larynx. (See “Vocal cord and larynx codes.”)

Tracheitis without obstructionJ04.10
Tracheitis with obstructionJ04.11
Supraglottitis without obstructionJ04.30
Supraglottitis with obstructionJ04.31
Nodules of vocal cordsJ38.2
Edema of larynxJ38.4
Laryngeal spasmJ38.5

Clinical scenario: A 40-year-old female presents to your office on Monday morning. She has an important business presentation later in the week and can barely speak. She gives you the history that her twin daughters were in a soccer tournament over the weekend and she spent two days cheering incessantly. She had no preceding symptoms of a viral upper respiratory infection. Your examination shows diffuse erythema of the larynx and vascular engorgement of the vocal folds. You recommend voice rest and adequate hydration and provide reassurance.

Your first thought is to code this as acute laryngitis, J04.0; however, this code falls in the J00-J06 range titled “Acute upper respiratory infections” and you see no evidence that this is an infective laryngitis. Therefore, you look up “hoarseness” in the ICD-10 index, and this takes you to R49.0, “Dysphonia.”


There are a few codes specific to the nose that you will commonly encounter in primary care. Infective rhinitis defaults to the “Acute nasopharyngitis” (common cold) J00 code, discussed earlier. However, chronic rhinitis gets its own code, J31.0. Vasomotor and allergic rhinitis also have their own code series (J30). (See “Rhinitis and other codes related to the nose.”)

Allergic rhinitis
Due to pollenJ30.1
Other seasonalJ30.2
Due to foodJ30.5
Due to animal hair and danderJ30.81
Nasal polypsJ33.0
Deviated nasal septumJ34.2
Hypertrophy of nasal turbinatesJ34.3

Clinical scenario: A father brings his 8-year-old daughter to your office because of allergy symptoms. He tells you that every fall she develops sneezing, a runny nose, and itchy eyes. The symptoms are worse when she is outdoors. The family recently adopted a dog from the local shelter, but the girl's symptoms do not seem worse. You make a diagnosis of allergic rhinitis and discuss conservative care including the use and overuse of decongestants and antihistamines.

You suspect this condition may be caused by pollen but have not performed allergy testing. The history suggests it is not related to the new pet or to food. You cannot use the “Other allergic rhinitis” code because it is used when the etiology is known but not listed in ICD-10. Therefore, you select J30.9, “Allergic rhinitis, unspecified.”

This is an example of the correct use of an “unspecified” code. It is being used per ICD-10 guidelines “when the information in the medical record is insufficient to assign a more specific code.” However, if in your clinical judgment the condition is caused by pollen, you need to document that judgment in the record and then assign code J30.1, “Allergic rhinitis due to pollen.”

Remember that ICD-10 does not prohibit you from using your clinical judgment, but your documentation must support your judgment.

Bronchitis and bronchiolitis

These two conditions are commonly encountered in the primary care office, but documenting the causative organism is rare, with the exception of J20.5, “Acute bronchitis due to respiratory syncytial virus” (RSV), in a pediatric patient. Therefore, you'll typically use just two ICD-10 codes: J20.9 and J21.9. (See “Bronchitis and bronchiolitis codes.”)

Acute bronchitis, unspecifiedJ20.9
Acute bronchiolitis, unspecifiedJ21.9

Influenza and pneumonia

As we move further down the respiratory tract, the likelihood of a primary care physician using diagnostic codes that specify the causative organism decreases, particularly in the office setting. When you make a clinical diagnosis of influenza in the office, coding will reflect an unidentified influenza virus. Therefore, depending on the presence of any additional findings, you will likely use one of several codes for “Influenza due to unidentified influenza virus.” (See “Influenza codes.”)

For influenza NOS (not otherwise specified), ICD-10 directs you to use J11.1. There are multiple additional codes for identified influenza virus infections, including novel A types (avian, swine, etc.).

Influenza due to unidentified influenza virus
With unspecified type of pneumoniaJ11.00
With other respiratory manifestationsJ11.1
With gastrointestinal manifestationsJ11.2
With otitis mediaJ11.83
With other manifestationsJ11.89

Community-acquired pneumonia is often a clinical diagnosis based on the history and physical examination, with no radiologic confirmation typically required or recommended on initial presentation. If your medical record documents findings consistent with pneumonia, you should code the visit as such rather than using sign and symptom codes. Remember that your clinical judgment and medical record documentation are the key elements that support your coding determination. In most cases, only one ICD-10 code will be applicable: J18.9, “Pneumonia, unspecified organism.”

Clinical findings might allow for increased coding specificity. In addition, there are numerous ICD-10 codes that should be used if a positive sputum culture has been documented. (See “Pneumonia codes.”)

Pneumonia, unspecified organismJ18.9
Additional clinical findings:
Bronchopneumonia, unspecified organismJ18.0
Lobar pneumonia, unspecified organismJ18.1
Hypostatic pneumonia, unspecified organismJ18.2
Other pneumonia, unspecified organismJ18.8
Positive sputum culture:
Viral pneumoniaJ12.0 - J12.9
Bacterial pneumoniaJ13 - J17


For these conditions, ICD-10 uses two base code categories: J43 for emphysema and J44 for chronic obstructive pulmonary disease (COPD). All codes require a fourth digit. However, without additional testing, it is unlikely that a primary care physician can clearly differentiate emphysema from chronic bronchitis. Per the National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health, “Most people who have COPD have both emphysema and chronic bronchitis. Thus, the general term ‘COPD’ is more accurate.”1 In that case, J44.9, “COPD, unspecified,” should be used. (See “Emphysema/COPD codes.”)

Other COPDJ44.X
COPD, unspecifiedJ44.9


Classification of asthma is based on the NHLBI's “Expert Panel Report 3: Guidelines for the Diagnosis and Management of Asthma” published in 2007. Coding is based on the classification level and the presence of an acute exacerbation or status asthmaticus. (See “Asthma codes.”)

UncomplicatedWith (acute) exacerbationWith status asthmaticus
Mild intermittentJ45.20J45.21J45.22
Mild persistentJ45.30J45.31J45.32
Moderate persistentJ45.40J45.41J45.42
Severe persistentJ45.50J45.51J45.52

Clinical scenario: A 23-year-old female presents to your office as a new patient. She states she is having problems with her asthma. Her past history included daily symptoms prior to being started on a low-dose inhaled corticosteroid with the need for short-acting beta agonist daily. With the use of the medications, her asthma had been well controlled prior to developing upper respiratory infection symptoms three days earlier. You make the diagnosis of an acute exacerbation of moderate persistent asthma (J45.41) and treat her accordingly.

At a follow-up visit one week later, she is symptom-free and tells you she has returned to her baseline status. An office FEV1 (test of forced expiratory volume in one second) is reduced about 5 percent. You confirm her diagnosis of moderate persistent asthma and code the visit using J45.40.

More to come

This completes our tour of the respiratory system codes. In the next installment in this series (see “Articles in FPM's ICD-10 series”), we'll head south and review documentation and coding for gastrointestinal disorders common in primary care.


You can access the following articles in FPM's ICD-10 topic collection:

"ICD-10: Major Differences for Five Common Diagnoses," FPM, September/October 2015.

"Digesting the ICD-10 GI Codes," FPM, January/February 2015.

"Coding Common Respiratory Problems in ICD-10," FPM, November/December 2014.

"The Anatomy of an ICD-10 Code," FPM, July/August 2012.

"ICD-10: What You Need to Know Now," FPM, March/April 2012.

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