The purpose of this study was to characterize the flagellin gene of Campylobacter jejuni and to study the structure of this protein and the regulation of its synthesis. A part of the flagellin gene of C. jejuni strain 81116 was recently cloned by us. This DNA fragment was used as a probe to isolate the other homologous flagellin sequences from genomic libraries. The flagellin nucleotide sequence was determined from overlapping clones. Two copies of the flagellin gene were identified: genes fla A and fla B consisted of 1731 base pairs each, occurred as tandem repeats, and were 95% identical. Only mRNA that was transcribed from gene A was detected in flagellate cells. sigma 28-specific promoter sequences were found upstream of the transcription initiation site. Analysis of the flagellin protein sequence showed that the amino-terminal and the carboxyl-terminal regions were highly similar to other bacterial flagellins. The conserved regions can form alpha-helices with a nonpolar backbone at one side. We suggest that because these domains were conserved (i) they may be involved in polymerization or transport of flagellins or both, and (ii) they are important for maturation and stability of the flagellum.