Johne's disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and has an economic impact on sheep productions. A shotgun proteomics study was carried out on terminal ileum tissues from infected and uninfected ewes. A large data set of proteomic changes occurring in the infected ileum was generated and analysed. MAP proteins highly expressed in vivo in the infected tissue were identified. The proteins undergoing the most relevant changes are related to host immune response and MAP pathogenesis.