Malignant tumors of the penis affect mainly the distal portion of the penis with the majority being squamous cell carcinomas (SCC). Several SCC histologic subtypes are recognized, each with distinctive clinicopathological and outcome features. These subtypes include usual SCC, warty, basaloid, warty-basaloid, papillary, verrucous, pseudoglandular, pseudohyperplastic, and sarcomatoid carcinomas. These malignant tumors begin as penile intraepithelial neoplasias (PeIN) and progress to infiltrate the erectile tissues and vascular spaces. Other epithelial tumors affecting the penis include extramammary Paget's disease, malignant melanoma, and clear cell carcinoma. Non-epithelial tumors, such as malignant lymphomas and sarcomas, can also be seen on occasion. The penis can also be affected by secondary tumors, mainly originating within the genitourinary or gastrointestinal tract. Pathological prognostic factors include histological grade and subtype, anatomical level of infiltration, perineural/vascular invasion, amongst others. In this chapter we cover the main macroscopic and microscopic features of these malignant lesions providing a unified framework for histopathologic diagnosis.