Methods for the specific and highly sensitive detection of Treponema pallidum infection comprising the use of specific antigenic proteins and peptides unique to Treponema pallidum are provided. In particular, detection assays based recognition of acidic repeat protein are provided. The methods of the present invention are useful for detection of primary syphilis at early stages of infection. In addition, the methods and compositions disclosed herein are directed to the differential detection of specific Treponema infections enabling the identification of causative agents for specific Treponema disease states: syphilis (Treponema pallidum subspecies pallidum), yaws (Treponema pallidum subspecies pertenue CDC-1 or CDC-2 strain), and bejel (Treponema pallidum subspecies endemicum).