We report two cases of anal cancer in patient with acquired immunodeficiency syndrome infected by human papillomavirus (HPV). One patient presented with huge anal abscess of long duration which developed after incomplete resection of anal warts 2 years ago and the other patient presented with anal bleeding. They were diagnosed as having anal squamous cell carcinoma. Highly oncogenic HPV 69 and 16 were detected by HPV-DNA chip on the previous specimen of warts and anal cancer tissue, respectively. The possibility of anal cancer should be considered in patients infected with human immunodeficiency virus who present anal problems such as anal abscess, anal bleeding, or condyloma accuminatum in anus.