The objectives of this study were to understand the molecular diversity of animal and human strains of Mycobacterium avium subsp. paratuberculosis isolated in the United States and to identify M. avium subsp. paratuberculosis-specific diagnostic molecular markers to aid in disease detection, prevention, and control. Multiplex PCR of IS900 integration loci (MPIL) and amplified fragment length polymorphism (AFLP) analyses were used to fingerprint M. avium subsp. paratuberculosis isolates recovered from animals (n ؍ 203) and patients with Crohn's disease (n ؍ 7) from diverse geographic localities. Six hundred bacterial cultures, including M. avium subsp. paratuberculosis (n ؍ 303), non-M. avium subsp. paratuberculosis mycobacteria (n ؍ 129), and other nonmycobacterial species (n ؍ 168), were analyzed to evaluate the specificity of two IS900 integration loci and a newly described M. avium subsp. paratuberculosis-specific sequence (locus 251) as potential targets for the diagnosis of M. avium subsp. paratuberculosis. MPIL fingerprint analysis revealed that 78% of bovine origin M. avium subsp. paratuberculosis isolates clustered together into a major node, whereas isolates from human and ovine sources showed greater genetic diversity. MPIL analysis also showed that the M. avium subsp. paratuberculosis isolates from ovine and bovine sources from the same state were more closely associated than were isolates from different geographic regions, suggesting that some of the strains are shared between these ruminant species. AFLP fingerprinting revealed a similar pattern, with most isolates from bovine sources clustering into two major nodes, while those recovered from sheep or humans were clustered on distinct branches. Overall, this study identified a high degree of genetic similarity between M. avium subsp. paratuberculosis strains recovered from cows regardless of geographic origin. Further, the results of our analyses reveal a relatively higher degree of genetic heterogeneity among M. avium subsp. paratuberculosis isolates recovered from human and ovine sources.Paratuberculosis or Johne's disease (JD) is a chronic granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (48). It is estimated that 35% of the U.S. herds are infected with M. avium subsp. paratuberculosis, resulting in annual losses of $200 million (7). Crohn's disease (CD) is also a chronic inflammation of distal intestines exhibiting a pathology similar to that of JD in ruminants. The prevalence of CD is estimated to be 0.15% among the U.S. population resulting in substantial morbidity and medical costs (1). M. avium subsp. paratuberculosis has been implicated as a cause of CD in humans (13,21,36). Currently, the evidence for a link remains inconclusive since strain sharing or a causal role of M. avium subsp. paratuberculosis has not been demonstrated.Comprehensive analysis of the molecular diversity and comparative molecular pathology of M. avium subsp. paratuberculosis will help establish the degree of heterog...