Background: In premenarchal children the diagnosis of vulvar condyloma is often based on the clinical or microscopic appearance of the lesions. Other techniques for diagnosing condyloma such as DNA subtyping are not always used by providers. The purpose of this study is to compare the microscopic examination and Human Papilloma Virus (HPV) DNA subtyping of vulvar specimens from premenarchal girls to determine whether DNA subtyping aids in the diagnosis process.Methods: Eleven premenarchal girls were taken to the operating room for the treatment of clinically diagnosed condyloma between 1993 and 1999 at the University of Michigan Medical Center. In all patients, tissue was sent for pathologic evaluation and in 10 patients the specimens also underwent DNA subtyping. One patient had prior DNA subtyping. All the other lesions were surgically ablated. Results: The average age of our patients at the time of surgery was 2.3 years, range 1-6 years. Four patients had prior surgical treatment and two patients had undergone prior medical treatment. The microscopic diagnosis was condyloma in 8 patients, squamous papilloma with focal koilocytosis not totally diagnostic for condyloma in 1 patient, chronic inflammatory infiltrate in 1 patient, and 1 patient had papillary squamous hyperplasia with no koilocytosis.All 11 specimens tested positive for HPV DNA, 10 specimens contained at least one of the low risk subtypes (6, 11, 42, 43, 44) and 1 tests positive for low risk as well as high risk HPV type (16, 18, 31, 33, 35, 45, 51, 52, 56).Conclusion: Although all our patients with a clinical diagnosis of condyloma tested positive for HPV DNA, only 8 of 11 were definitely diagnosed with condyloma by microscopic examination. We therefore suggest that in premenarchal patients with verrucous lesions in the anogenital area HPV DNA subtyping be considered to avoid confusion with the diagnosis.