Penile cancer (CP) is a rare disease, closely linked to poor penis hygiene and is more prevalent in regions with low socioeconomic status. In Brazil, the CP represents about 2 to 4% among all types of cancer in men, being more frequent in the north and northeast regions. The discovery of the molecular mechanisms involved in the genesis of several tumors has led to earlier diagnoses and improved efficiency of procedures. The absence of studies with large-scale sequencing in the CP motivates our study. Thus, the objective of the work is to make a study of the exome of CP tissue. For this work, tumor tissue samples from patients diagnosed with penile squamous cell carcinoma were selected.The DNA had the exome sequenced and the data were analyzed via bioinformatics.Moleculares diagnoses were also made for HPV 16 and 18, which is a risk factor for CP.As a result, we found a very heterogeneous sample, however, the finding of mutations in genes responsible for important processes for the maintenance and health of cells were found. We observed 40% of patients with mutations in NOTCH family, genes related to cell differentiation, proliferation and survival, we also found the presence of TP53 and ATM genes important for cell mutation repair in patients with a worse prognosis. The most mutated genes were PABPC1, MUC16, USP6 and SIRPa, both in patients and in controls, which possibly rules out important roles in CP. Some mutations found in patients with poor prognosis were exclusive to these patients, an important data that provides a new study source for these variations. Regarding HPV, we found in only 16.67% of patients what is less than that found in the literature. These data are important because they can help us to understand the appearance and evolution of CP.