Primary squamous cell carcinoma (SCC) of the colorectum is a rare malignancy of unknown etiology and pathogenesis. We report a case of primary SCC of the rectum. A 55-year-old man with a rectal tumor and human immunodeficiency virus (HIV) infection was referred to our hospital. Histopathology of biopsy specimens showed characteristics of SCC. We diagnosed the patient as having primary moderately differentiated SCC of the rectum according to the criteria proposed by Cooper. Human papillomavirus (HPV) DNA was amplified by polymerase chain reaction analysis of unfixed tumor biopsy specimens. In addition, no p53 overexpression or nuclear staining of retinoblastoma protein (Rb) was observed in neoplastic cells by immunohistochemical staining. We suggest from our case that HPV infection following the inactivation of the cellular tumor suppressor Rb and the immune suppression induced by HIV infection play an etiologic role in the pathogenesis of rectal SCC, consistent with the well-established concept of HPV-associated anal carcinogenesis.