ABSTRACTJohne's disease in ruminants is caused byMycobacterium aviumsubsp.paratuberculosis. Diagnosis ofM. aviumsubsp.paratuberculosisinfection is difficult, especially in the early stages. To date, ideal antigen candidates are not available for efficient immunization or immunodiagnosis. This study reports thein silicoselection and subsequent analysis of epitopes ofM. aviumsubsp.paratuberculosisproteins that were found to be upregulated under stress conditions as a means to identify immunogenic candidate proteins. Previous studies have reported differential regulation of proteins whenM. aviumsubsp.paratuberculosisis exposed to stressors which induce a response similar to dormancy. Dormancy may be involved in evading host defense mechanisms, and the host may also mount an immune response against these proteins. Twenty-fiveM. aviumsubsp.paratuberculosisproteins that were previously identified as being upregulated underin vitrostress conditions were analyzed for B and T cell epitopes by use of the prediction tools at the Immune Epitope Database and Analysis Resource. Major histocompatibility complex class I T cell epitopes were predicted using an artificial neural network method, and class II T cell epitopes were predicted using the consensus method. Conformational B cell epitopes were predicted from the relevant three-dimensional structure template for each protein. Based on the greatest number of predicted epitopes, eight proteins (MAP2698c [encoded bydesA2], MAP2312c [encoded byfadE19], MAP3651c [encoded byfadE3_2], MAP2872c [encoded byfabG5_2], MAP3523c [encoded byoxcA], MAP0187c [encoded bysodA], and the hypothetical proteins MAP3567 and MAP1168c) were identified as potential candidates for study of antibody- and cell-mediated immune responses within infected hosts.