Campylobacter jejuni isolates of human, canine, feline, bovine and poultry origin were investigated for their genomic diversity using O-antigen typing (n = 271), SmaI (n = 158) and XhoI (n = 158) macrorestriction analysis and ERIC–PCR (n = 107). The O-antigens O[ratio ]1/44, O[ratio ]2, O[ratio ]4 complex, O[ratio ]37, O[ratio ]40 were identified and 53.7% of the human and 56.1% of the animal strains were typable with the available antisera. Two ERIC–PCR pattern groups were generated representing human and animal strains as well as those exclusively of animal origin. XhoI macrorestriction analysis also distinguished ‘human’ and ‘non-human’ strain clusters, but by SmaI restriction mainly serotype-associated clusters were found. In conclusion, genomic differences may occur between ‘human’ and ‘non-human’ strains and this may reflect their potential to overcome the barrier from animals to humans.