BACKGROUND We compare features of two similar nevi which may be confused with melanoma: deep penetrating nevus (DPN), and nevus with focal atypical epithelioid component (NFAEC). METHODS Clinical/demographic and histologic information regarding 146 DPN and 81 NFAEC were compared. Patient outcomes were ascertained via a questionnaire solicited to the referring physicians. RESULTS Clinical features were similar for each type of nevus. Histologically, all lesions demonstrated identical aggregates of epithelioid melanocytes. DPN more often extended into the deep dermis or subcutaneous tissue, while NFAEC was typically confined to the superficial dermis. NFAEC more often demonstrated a junctional component (P < .001) and coexistent common nevus with congenital features (P = .035). DPN more often demonstrated adnexal spread (P < .001). A subgroup with overlapping features was identified. With an average of 6.4 years follow-up, there were just two recurrences, and no metastases. CONCLUSIONS This retrospective study utilized tissue specimens from a single reference laboratory; ergo, some inherent selection bias exists. Specimens were randomly selected for P53 immunostaining, leading also to potential sampling error. CONCLUSIONS DPN and NFAEC show considerable similarity, differing mainly in the depth of extent for the lesion. It is possible that NFAEC represents a more superficial variant of DPN. A subgroup with overlapping features, but intermediate depth, supports such a relationship.