Condylomata acuminata commonly have horn cysts and resemble seborrheic keratoses. The two are differentiated by areas of compact stratum corneum, round parakeratosis, coarse hypergranulosis, and vacuolated keratinocytes with large gray nuclei. In situ hybridization can identify the human papillomavirus (HPV) type.

Bowenoid papulosis presents as discrete pink, brown, or gray lesions in the genitalia. They are typically sessile, rather than papillomatous or cauliflower-like. The histologic spectrum ranges from that of a condyloma with buckshot scatter of atypical cells to full-thickness atypia, indistinguishable from Bowen’s disease.