Buruli ulcer is a devastating condition emerging in West Africa. We investigated why patients often report late to the hospital. Health seeking behaviour determinants and stigma were studied by in-depth interviews in patients treated in hospital (n=107), patients treated traditionally (n=46) of whom 22 had active disease, and healthy community control subjects (n=107). We developed a model capturing internal and external factors affecting decision making. With increasing severity, extent and duration of Buruli ulcer, a shift of influencing factors on health seeking behaviour appears to occur. Factors causing delay in presenting to hospital were the use of traditional medicine before presenting at the treatment centre; costs and duration of admission; disease considered not serious enough; witchcraft perceived as the cause of disease; and fear of treatment, which patients expected to be amputation. This study confirms the importance of self-treatment and traditional healing in this area. Our study was performed before antimicrobial treatment was introduced in Benin; we suggest that this model and the results from this analysis should be used as a baseline from which to measure the influence of the introduction of antimicrobial treatment on health seeking behaviour for Buruli ulcer in Benin.