This study aimed to determine the distribution of Buruli ulcer (BU) in Lalo, one of the endemic districts of the Couffo department in Bénin. A total of 752 BU patients were detected in this district with 160 active and 592 inactive cases. The overall prevalence of BU in this district is 86.6 per 10,000 inhabitants, varying from 0 to 249/10,000 between sub-districts. At village level the prevalence varies between 0 and 561 cases per 10,000 inhabitants. Our findings confirm the large variation of distribution of the disease at the village level in endemic area. Children under 15 years are frequently affected. We also found a significant association between age and location of Buruli lesions. Further epidemiological and environmental studies are needed to identify the reasons for the extraordinary variation in BU distribution between villages from the same sub-district, and to confirm if it is associated with temporal variations.