Home » Coding guidelines for Urine Culture – CPT 87086, 87088

Coding guidelines for Urine Culture – CPT 87086, 87088

cpt code 87088

A bacterial urine culture is a laboratory procedure performed on a urine specimen to establish the probable etiology of a presumed urinary tract infection. It is common practice to do a urinalysis prior to a urine culture. A urine culture may also be used as part of the evaluation and management of another related condition. The procedure includes aerobic agar-based isolation of bacteria or other cultivable organisms present, and quantification of types present based on morphologic criteria. Isolates deemed significant may be subjected to additional identification and susceptibility procedures as requested by the ordering physician. The physician’s request may be through clearly documented and communicated laboratory protocols.

Indications and Limitations of Coverage CPT Code 87088

IndicationsUrine Culture and Sensitivity CPT Code

A patient’s urinalysis is abnormal suggesting urinary tract infection, for example, abnormal microscopic (hematuria, pyuria, bacteriuria); abnormal biochemical urinalysis (positive leukocyte esterase, nitrite, protein, blood); a Gram’s stain positive for microorganisms; positive bacteriuria screen by a non-culture technique; or other significant abnormality of a urinalysis. While it is not essential to evaluate a urine specimen by one of these methods before a urine culture is performed, certain clinical presentations with highly suggestive signs and symptoms may lend themselves to an antecedent urinalysis procedure where follow-up culture depends upon an initial positive or abnormal test result.

A patient has clinical signs and symptoms indicative of a possible urinary tract infection (UTI). Acute lower UTI may present with urgency, frequency, nocturia, dysuria, discharge or incontinence. These findings may also be noted in upper UTI with additional systemic symptoms (for example, fever, chills, lethargy); or pain in the costovertebral, abdominal, or pelvic areas.  Signs and symptoms may overlap considerably with other inflammatory conditions of the genitourinary tract (for example, prostatitis, urethritis, vaginitis, or cervicitis). Elderly or immunocompromised patients, or patients with neurologic disorders may present atypically (for example, general debility, acute mental status changes, declining functional status).

The patient is being evaluated for suspected urosepsis, fever of unknown origin, or other systemic manifestations of infection but without a known source. Signs and symptoms used to define sepsis have been well established.

A test-of cure is generally not indicated in an uncomplicated infection. However, it may be indicated if the patient is being evaluated for response to therapy and there is a complicating co-existing urinary abnormality including structural or functional abnormalities, calculi, foreign bodies, or ureteral/renal stents or there is clinical or laboratory evidence of failure to respond as described in Indications 1 and 2.

In surgical procedures involving major manipulations of the genitourinary tract, preoperative examination to detect occult infection may be indicated in selected cases (for example, prior to renal transplantation, manipulation or removal of kidney stones, or transurethral surgery of the bladder or prostate).

Urine culture may be indicated to detect occult infection in renal transplant recipients on immunosuppressive therapy.


CPT 87086 may be used one time per encounter.

Colony count restrictions on coverage of CPT 87088 do not apply as they may be highly variable according to syndrome or other clinical circumstances (for example, antecedent therapy, collection time, degree of hydration).

CPT 87088, 87184, and 87186 may be used multiple times in association with or independent of CPT 87086, as urinary tract infections may be polymicrobial.

Testing for asymptomatic bacteriuria as part of a prenatal evaluation may be medically appropriate but is considered screening and, therefore, not covered by Medicare. The US Preventive Services Task Force has concluded that screening for asymptomatic bacteriuria outside of the narrow indication for pregnant women is generally not indicated. There are insufficient data to recommend screening in ambulatory elderly patients including those with diabetes. Testing may be clinically indicated on other grounds including likelihood of recurrence or potential adverse effects of antibiotics, but is considered screening in the absence of clinical or laboratory evidence of infection.

Specific coding guidelines | CPT Code for Urine Culture:

a.  Use CPT 87086 Culture, bacterial, urine; quantitative, colony count where a urine culture colony count is performed to determine the approximate number of bacteria present per milliliter of urine. The number of units of service is determined by the number of specimens.

b.  Use  CPT  87088  where  a  commercial  kit  uses  manufacturer  defined  media  for isolation, presumptiveidentification, and quantitation of morphotypes present. The number of units of service is determined by the number of specimens.

c.  Use  CPT  87088  where  identification  of  morphotypes  recovered  by  quantitative culture or commercial kits and deemed to represent significant bacteriuria requires the use of additional testing, for example, biochemical test procedures on colonies. Identification based solely on visual observation of the primary media is usually not adequate to justify use of this code. The number of units of service is determined by the number of isolates.

d.  Use  CPT  87184  or  87186  where  susceptibility  testing  of  isolates  deemed  to  be significant  is  performed  concurrently  with  identification.  The  number  of  units  of service is determined by the number of isolates. These codes are not exclusively used for urine cultures but are appropriate for isolates from other sources as well.

e.  Appropriate combinations are as follows: CPT 87086, 1 per specimen with 87088, 1 per isolate and 87184 or 87186 where appropriate.

f.  Culture for other specific organism groups not ordinarily recovered by media used for  aerobic urine  culture  may  require  use  of  additional  CPT  codes  (for  example, anaerobes from suprapubic samples).

g.  Identification  of  isolates  by  non-routine,  nonbiochemical  methods  may  be  coded appropriately (for example, immunologic identification of streptococci, nucleic acid techniques for identification of N. gonorrhoeae).

h.  While infrequently used, sensitivity studies by methods other than CPT 87184 or 87186 are appropriate. CPT 87181, agar dilution method, each antibiotic or CPT 87188, macrotube dilution method, each antibiotic may be used. The number of units  of  service  is  the  number  of  antibiotics  multiplied  by  the  number  of  unique isolates.

2.  ICD-9-CM  code  780.02,  780.9  or  799.3  should  be  used  only  in  the  situation  of  an elderly  patient,  immunocompromised  patient  or  patient  with  neurologic  disorder  who presents without typical manifestations of a urinary tract infection but who presents with one of the following signs or symptoms, not otherwise explained by another co-existing condition:  increasing  debility;  declining  functional  status;  acute  mental  changes; changes in awareness; or hypothermia.

3.  In cases of post renal-transplant urine culture used to detect clinically significant occult infection in patients on long term immunosuppressive therapy, use code V58.69.

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