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Most penile neoplasms are squamous cell carcinomas (SCC), but there are subtypes that show morphologic and possibly etiologic differences. Clinicopathologic features of 20 patients with basaloid carcinoma (BC), an unusual variant of squamous cell carcinoma, are presented. Median age was 52 years, and all tumors were located in the glans, three confined to the perimeatal region. Average tumor size was 3.8 cm. Microscopically, nests of small, basophilic cells with numerous mitosis were present. Human papillomavirus DNA sequences (type 16), using the polymerase chain reaction (PCR), were found in 9 of 11 cases. Differential diagnosis included urethral transitional cell, basal cell, small cell neuroendocrine, and metastatic carcinoma. Factors more significantly associated with regional metastasis and mortality were tumor thickness greater than 10 mm and infiltration of the corpus cavernosum. A comparison with typical squamous cell carcinoma showed basaloid carcinoma to have a higher histologic grade, a deeper invasion of penile anatomic levels, and a higher mortality rate. Of 17 patients observed, 10 were dead of disease (average time, 34 months), one was alive with disease 6 months after diagnosis, and 5 were alive and free of disease (average time, 71 months); the remaining patient died of other causes. Basaloid carcinoma is a distinctive morphologic subtype of squamous cell carcinoma frequently associated with the human papilloma virus.