Johne's Disease is a chronic, granulomatous enteritis of ruminant animals caused by Mycobacterium avium subspecies paratuberculosis. Unfortunately, available diagnostic tests cannot reliably detect animals in early stages of disease, hampering current control efforts which rely heavily on testing and culling of infected animals. In this work, two families of polymorphic proteins, the PE and PPE proteins, were tested for their potential as immunodiagnostic targets. These proteins are cell-surface exposed and hypothesized to be involved in virulence and antigenic variation. Using a bioinformatic approach, a number of highly specific sequences of potential diagnostic utility were identified within these two families. Representatives of the families were expressed and studied using in vitro transcription/translation, as well as recombinant expression and co­expression in E. coli. Both humoral and cell-mediated immune assays were then conducted on the expressed products using whole blood and sera from naturally-infected cattle and several potential diagnostic targets were identified.