Molecular characterization of Mycobacterium avium subspecies paratuberculosis strains is a helpful tool for a better understanding of the epidemiology. Therefore, several molecular techniques have been tested for their suitability to differentiate M.a.p strains isolated from different animal species in the last decade. The objective of this study was to characterise caprine M. a. paratuberculosis strains from different geographical locations by Pulsed Field Gel Electrophoresis (PFGE), Restriction Fragment Length Polymorphism and hybridisation to IS900 (RFLP-IS900) and IS1311 Polymerase Chain Reaction-Restriction Enzyme Analysis (PCR-REA) to determine the genetic variation amongst the caprine isolates and the relationship with strains isolated from other animal species. The study included 38 caprine isolates of M.a.p from Spain (n=25), Scotland UK (n=11) and Norway (n=3). All the isolates were subjected to PCR analysis for IS1311 combined with restriction analysis (Hinf I and Mse I) according to Marsh et al. 1999. All the samples studied were found to be of the cattle (C) type with the exception of two Spanish strains that were of the sheep (S) type. DNA for PFGE and RFLP analysis was prepared from stirred broth cultures of M.a.p isolates and restricted with SnaB I and Spe I (for PFGE) and BstE II and Pvu II (for RFLP-IS900). Combination of PFGE and RFLP results obtained with both restriction enzymes gave a total of 12 and 6 'multiplex' profiles, respectively. Novel profiles were identified with both techniques. The data were subjected to phylogenetic analysis, which revealed that the caprine isolates have an interesting genetic relationship with respect to strains isolated from other animal species. Attendance to this Congress was sponsored by the EU-funded project FAIR6-CT98-4373.