Diagnosis of basaloid squamous carcinoma (BSCC) currently relies mainly on histological criteria, with variable immunohistochemical results reported in small series. We explored the use of a battery of immunohistochemical stains to elucidate this diagnosis on 45 cases of BSCC. To further elucidate the immunohistochemical profile of BSCC, to explore potential genetic pathways of malignant transformation using proliferation markers, and to investigate a possible link with Human Papillomavirus (HPV). Forty-five cases of BSCC and 34 site-matched cases of squamous cell carcinoma (SCC) were obtained from the archives of the pathology department at our institution. Extensive literature review was undertaken utilizing Medline. Ber-EP4 is a useful diagnostic marker for BSCC, positive in 82% (37/45) of the cases and in 68% (23/34) of SCC. An alternative is the combination of cytokeratins CK14 and CK7, known to be negative, and CK1, known to be positive, which achieves an accuracy of 73% (33/45) in BSCC and 88% (30/34) in SCC. The two diagnostic approaches were in agreement in 66% of the cases; both methods were equally accurate in the divergent cases. Increased expression of the proliferation markers supports the concept that BSCC is a rapidly growing tumor. Results of p16 stains support an etiological link between BSCC and HPV; interestingly, HPV was present significantly more in BSCC (71% (32/45)), than in SCC (59% (20/34)) in this study (P=0.02).