OBJECTIVE: To estimate the prevalence and pattern of conjuctival squamous cell carcinoma (CSCC) in patients with HIV infection. DESIGN: A hospital based cross sectional study. SETTING: Kenyatta National Hospital (KNH) and Kikuyu Eye Unit (KEU) during the period November 2003 and May 2004. SUBJECTS: Four hundred and nine HIV positive patients. RESULTS: Four hundred and nine HIV positive patients aged 25 to 53 years were screened. Male to Female ratio was 1:1. One hundred and three had conjunctival growths. Thirty two had histologically proven conjunctiva squamous cell carcinoma (CSCC). Estimated prevalence of CSCC among HIV positive patients was 7.8%. The average duration of growth of the conjunctival masses was 21.8 months. The average size of the lesions at the time of presentation was 6.6 mm. Twenty two (68.8%) patients had primary CSCC, while ten (31.2%) had recurrent lesions. The pattern of the histopathology results was: fifteen (46.9%) patients had poorly differentiated squamous cell carcinoma; nine (28%) had moderately differentiated squamous cell carcinoma; five patients (15.6%) had CIN; two patients (6.3%) had dysplasia and one patient (3.1%) had a well differentiated squamous cell carcinoma. CONCLUSIONS: Prevalence of CSCC in HIV/AIDS patients was 7.8%. Patients present late with advanced lesions. Recurrence rates from previous surgery are high. The often uncharacteristic complaints and findings on presentation complicate the clinical diagnosis. Active search for early manifestations of CSCC in HIV / AIDS patients, complete surgical excision and close follow up is necessary. Alternative treatment methods and techniques like the topical use of antimetabolites should be explored further.