Traditionally, due to its low cost, ready availability, and proved diagnostic accuracy, ultrasonography (US) has been the primary imaging modality for the evaluation of scrotal and, to a lesser extent, penile disease. However, US is limited by its relatively small useful field of view, operator dependence, and inability to provide much information on tissue characterization. Magnetic resonance (MR) imaging, with its excellent soft-tissue contrast and good spatial resolution, is increasingly being used as both a problem-solving tool in patients who have already undergone US and as a primary modality for the evaluation of suspected disease. Specifically, MR imaging can aid in differentiating between benign and malignant lesions seen at US, help define the extent of inflammatory processes or traumatic injuries, and play a vital role in locoregional staging of tumors. Consequently, it is becoming more important for radiologists to be familiar with the wide range of penile and scrotal disease entities and their MR imaging appearances. The authors review the basic anatomy of the penis and scrotum as seen at MR imaging and provide a basic protocol for penile and scrotal imaging, with emphasis on the advantages of MR imaging. Pathologic processes are organized into traumatic (including penile fracture and contusion), infectious or inflammatory (including Fournier gangrene and scrotal abscess), and neoplastic (including both benign and malignant scrotal and penile tumors) processes.