Although vaccines against Bordetella pertussis, the causative agent of whooping cough, have been in use for over 50 y, the disease has remained endemic and is still a public health problem in many countries. It has been shown that antibody titres against pertactin, which is 1 of the exposed virulence factors of pertussis, correlate with protection and pertactin is now 1 of the components of most acellular pertussis vaccines. However, little is known about the structure and location of protective epitopes on pertactin. Here we set out to investigate the antibody response using naturally occurring pertactin variants and deletion derivates. We found the N-terminus of pertactin to be immunodominant in both rabbits and humans. In contrast to vaccinated rabbits, we could not detect pertactin type-specific antibodies in human sera. In conclusion, these results show for the first time to which defined regions of the pertactin molecule antibody responses are induced. It also suggests that the amount of pertactin type-specific antibodies will not be very large and that the variation in pertactin probably will not constitute a problem in highly immune individuals.