Pagetoid dyskeratosis is a benign incidental pathologic finding that has been reported in many distinct skin lesions on various locations of the body. A man who had pagetoid dyskeratosis within lesions of the penile shaft is described and similar cases of pagetoid dyskeratosis in lesions of the male genitalia are reviewed. The patient was a 26-year-old healthy man who developed several asymptomatic penile papules that were refractory to topical imiquimod 5% cream and cryotherapy. Snip biopsies were performed and microscopic examination revealed pagetoid dyskeratosis. PubMed was searched for the following terms: cell, clear, dyskeratosis, genitalia, pagetoid, penile, penis, prepuce, scrotum, and shaft. The papers containing these terms and their references were reviewed. Pagetoid dyskeratosis has been observed in lesions on the prepuce and scrotum; this case report now expands the distribution of this finding to the penile shaft. Clinicians and pathologists should be aware of this intriguing potential incidental finding within skin lesions of the male genitalia.