Campylobacter jejuni isolates obtained from pets housed in shelters and in private households were subtyped by fla typing (using DdeI and HinfI restriction enzymes) and pulsed-field gel electrophoresis (PFGE) techniques. Composite fla cluster analysis on 78 C jejuni isolates was more discriminative than either single fla typing technique with 39.7 per cent single isolate patterns. PFGE on 52 C jejuni isolates revealed 53.8 per cent single isolate patterns and was the most discriminative method applied. A database of C jejuni subtyping profiles from pets in Ireland was assembled. The presence of genetic heterogeneity detected in the C jejuni subtypes suggests that pets can acquire the organisms from multiple potential sources. In addition, heterogeneity was detected in the C jejuni subtypes obtained by different culture methods within the same pet. There was a link between isolates from dogs in close contact in the same environment, confirming that this is a potential route of infection, and clusters were detected containing both cat and dog C jejuni isolates, suggesting possible interspecies transmission.