•First incidence rates from a population-based cancer registry in Cotonou, Benin.•Breast and cervical cancers account for half of all cancers in women.•Incidence of breast is 50% higher than cervix; cases occur in rather younger women.•Prostate was most common cancer of men, as in other West African countries.•Results compared with other West/Central African countries &black population of USA. Incidence data from the population cancer registry of Cotonou (Benin) for the three year period 2014–2016 are presented. 1086 cancer cases were recorded, 608 cases (56.0%) in women (corresponding to an age standardized incidence rate (ASR) of 78.4 per 100,000) and 478 cases (44.0%) in men (ASR 91.8 per 100,000). Breast and cervical cancer accounted for 49.2% of all cancers in women. Breast cancer (ASR 22.6 per 100,000) was more common than cervical cancer (ASR 14.9 per 100,000) and the mean age of cases was lower. The incidence of prostate cancer (one quarter of all cancers in men), 30.5 per 100,000, was similar to that in other West African registries. Cancers of the liver and digestive tract were also relatively common in both sexes. These are the first data on cancer incidence in Benin, and will be invaluable for the development and evaluation of the National Cancer Control plan.