Within the field of study of the origins of syphilis (pre-Columbian, Columbian and Unitary hypotheses), this work aims to identify, through a systematic approach, treponematoses in several archaeological sites from the south and southeast coast of Brazil. 768 skeletons from 45 shell mounds (sambaquis) were investigated using an integrated morphoscopic method to diagnose treponematoses (syphilis, yaws and bejel). 22 (2.86%) suspected cases of treponematosis were detected in 14 of the 45 evaluated sites (31.11%). After the differential diagnosis, four cases of acquired syphilis, nine cases of yaws and nine individuals with treponematosis without definitive diagnosis were identified. Eleven new 14C AMS dates obtained from individuals with lesions compatible with treponematoses show that this disease spectrum affected people from 6300 years BP to 500 years BP. This study suggests the existence of treponematoses at the Brazilian southeast coast about 6000 years before the European contact.