Condyloma acuminatum (CA) is caused by human papilloma virus (HPV) infection, and it often occurs in the genital and perianal regions. The subtypes of HPV mainly include HPV-6, -11, -16, and -18. This case report presents a 37-year-old woman admitted to hospital because of lower abdominal pain and increased stool frequency for > 1 year. Colonoscopy found a neoplasm with a diameter ~5 mm in the rectum, ~5 cm from the anal margin. The pathological diagnosis of the excised specimen was CA. HPV DNA analysis indicated HPV-6. After asking the history closely, the patient admitted that her husband had CA, and they once had anal intercourse. The patient was discharged on the third day after the operation, and she was referred to a dermatology and venereal disease specialist for further treatment.