Basal cell carcinoma (BCC) occurring on non-sun-exposed sites, especially the perianal and genital regions, is very rare. We analyzed the incidence, clinical and pathologic features, and etiologic and prognostic factors of all non-nevoid perianal and genital BCCs diagnosed at our institution within a defined period (January 1985-September 1996). A retrospective review was performed with the use of patient clinical records and dermatopathologic slides. Cutaneous biopsy samples were tested for the presence of human papillomavirus (HPV) by in situ hybridization using biotinylated pan-HPV and serotype-specific (6, 11, 16, 18, 31, 33, 51) probes. Of all non-nevoid BCC syndrome cases, 51 BCCs (0.27%) were located within the perianal and genital regions. The average age of the patients was 73 years. Nine perianal BCCs occurred in men, 6 in women. Ten BCCs occurred in the pubic area, 18 on the vulva, 6 on the scrotum, and 2 on the penis. Three patients had 2 tumor sites. The average size of BCC was 1.95 cm; 29.4% were ulcerated. Seventeen patients (36%) had a history of skin cancer on sun-exposed sites and 10 (21%) had a possibly relevant associated condition. HPV was not detected in the specimens tested. Treatments included wide excision (n = 32), electrodesiccation and curettage (n = 10), Mohs micrographic surgery (n = 8), and carbon dioxide laser (n = 1). Of 30 patients with 5 years' follow-up or longer, 1 recurrence was noted 7 years after wide excision. There were no metastases. BCC of the perianal and genital skin is rare and exhibits clinical and histologic heterogeneity. Advancing age and local trauma may contribute to the pathogenesis of BCC at these sites.