Background. Advanced penile squamous cell carcinoma (PSCC) is associated with poor survival due to the aggressiveness of the disease and lack of effective systemic therapies. Comprehensive genomic profiling (CGP) was performed to identify clinically relevant genomic alterations (CRGAs). Materials and Methods. DNA was extracted from 40 mm of formalin-fixed, paraffin-embedded sections in patients with advanced PSCC. CGP was performed on hybridizationcaptured, adaptor ligation-based libraries to a mean coverage depth of 6923 for 3,769 exons of 236 cancerrelated genes plus 47 introns from 19 genes frequently rearranged in cancer. CRGAs were defined as genomic alterations (GAs) linked to targeted therapies on the market or under evaluation in mechanism-driven clinical trials.