Introduction Elevated serum beta human chorionic gonadotrophin (β-hCG) in a female normally indicates pregnancy or possibly, gestational trophoblastic disease or ovarian germ cell tumours. Expression of β-hCG has been demonstrated in cervical and endometrial carcinoma and other non-germ cell tumours of the ovary, vulva, breast, prostate, lung, colon, oral/facial tissue and stomach. Case report We report a 43-year-old premenopausal woman with p16 positive squamous cell anal cancer. Pre-treatment urinary screening was positive for β-hCG (218 IU/L), which was confirmed on serum and expressed in the tumour. Pelvic ultrasound ruled out pregnancy. Cervical cytology detected human papilloma virus p16 infection and a potential squamous intraepithelial lesion. Management and outcome: She received definitive chemoradiation (Mitomycin/5-fluorouracil) for six weeks. β-hCG, taken four weeks post completion, had returned to normal levels (<2 IU/L). Discussion Cases of elevated serum β-hCG are documented in different cancers including breast, gastric, lung, ovarian and renal cell. In our case, the elevated β-hCG is probably ectopic excretion by the squamous cell carcinoma tumour in the anus. While this has never been reported previously in the anus, it is likely due to the documented risk of development of precancerous as well as cancerous anal and cervical lesions through human papilloma virus infection. Raised levels of β-hCG have been reported in cervical cancers. Other possible causes of β-hCG elevation were excluded. Following treatment, her β-hCG level returned to normal strengthening the hypothesis that β-hCG elevation was due to the anal carcinoma. In conclusion, unexplained ectopic secretion of β-hCG may be the first sign of a primary malignancy.