Genotypes were analysed within 29 geographically diverse strains of Campylobacter jejuni mainly from human enteritis cases and four strains representing C. coli, C. lari and C. helveticus. A 1723 bp DNA fragment, amplified by the polymerase chain reaction (PCR) from the flagellin (fla) genes, was used to probe genomic Southern blots for restriction site variation at homologous loci. Internal Hin fl restriction fragment length polymorphisms (RFLP) of the fla gene PCR amplification product were also used to characterize isolates. Copy number and polymorphisms in and around the fla genes were detected, and strains were grouped into 10 genotypes on the basis of fla restriction site similarities. Campylobacter jejuni had a fla gene copy number of two and the majority (64%) of strains in the species had common internal fla gene sequences as indicated by Hin fl restriction analysis. A greater degree of diversity was detected around the fla loci in Hae III and Bgl II genomic Southern blots. The results showed that analysis of fla genes provided a novel and fundamental approach to grouping strains and offered a basis for defining a predominant clonal evolutionary line within C. jejuni.