Penile squamous cell carcinoma (PSCC) is rare; hence little is known about its aetiology and pathogenesis. Two challenges exist in the clinical management of PSCC patients. Firstly, finding a non-invasive method to aid the detection of occult lymph node metastasis to improve patient selection for inguinal lymphadenectomy. Secondly, the development of novel treatment strategies for those with advanced PSCC, as current treatment options are limited. A high prevalence of copy number gain in the chromosome 3q arm has been identified and linked to poor cancer-specific and disease-free survival in PSCC. Within this region lies the PIK3CA oncogene, which is mutated/amplified/gained and results in the activation of the PI3K-AKT-mTOR pathway. PIK3CA copy number gain has not been fully investigated in PSCC and it has the potential to be a driver gene in penile carcinogenesis and the PI3K-AKT-mTOR pathway presents an opportunity for targeted therapeutics in PSCC. I demonstrated an increasing frequency of PIK3CA copy number gain with evolving PSCC disease state (penile intraepithelial neoplasia (10/58; 17%), primary PSCC (83/199; 42%), advanced primary PSCC (20/26; 77%); p < 0.0001) with few PIK3CA mutations in PSCC (3/51; 6%). PIK3CA copy number gain correlated with more aggressive PSCC subtypes (p=0.0028), higher tumour grade (p < 0.0001) and stage (p=0.0043) and thus could be used as a marker of high-risk disease. However, it shows no significant association with lymph node metastasis or prognostic value for cancer-specific survival in PSCC. Overall, I confirmed that the PI3K-AKT-mTOR pathway activity is primarily involved in early penile carcinogenesis and based on these findings the therapeutic targeting of this pathway in those with advanced PSCC disease is unlikely to produce significant clinical benefit. Future studies will need to focus on the identification of new clinically relevant candidate genes and signalling pathways, which offer prognostic value and the potential for targeted therapeutics in this rare cancer.