Many virulence factors secreted from pathogenic gram-negative bacteria are autotransporter proteins. The final step of autotransporter secretion is C -> N-terminal threading of the passenger domain through the outer membrane (OM), mediated by a co-translated C- terminal porin domain. The native structure is formed only after this final secretion step, which requires neither ATP nor a proton gradient. Sequence analysis reveals that, despite size, sequence, and functional diversity amongst autotransporter passenger domains, >97% are predicted to form parallel β-helices, indicating this structural topology may be important for secretion. We report the folding behavior of pertactin, an autotransporter passenger domain from Bordetella pertussis. The pertactin β-helix folds reversibly in isolation, but folding is much slower than expected based on size and native state topology. Surprisingly, pertactin is not prone to aggregation during folding, even though folding is extremely slow. Interestingly, equilibrium denaturation results in the formation of a partially folded structure, a stable core comprising the C-terminal half of the protein. Examination of the pertactin crystal structure does not reveal any obvious reason for the enhanced stability of the C-terminus. In vivo, slow folding would prevent premature folding of the passenger domain in the periplasm, prior to OM secretion. Moreover, the extra stability of the C-terminal rungs of the β-helix might serve as a template for the formation of native protein during OM secretion; hence vectorial folding of the β-helix could contribute to the energy-independent translocation mechanism. Coupled with the sequence analysis, the results presented here suggest a general mechanism for autotransporter secretion.