We examined two variants of the genome-sequenced strain,Campylobacter jejuniNCTC11168, which show marked differences in their virulence properties including colonization of poultry, invasion of Caco-2 cells, and motility. Transcript profiles obtained from whole genome DNA microarrays and proteome analyses demonstrated that these differences are reflected in late flagellar structural components and in virulence factors including those involved in flagellar glycosylation and cytolethal distending toxin production. We identified putative σ28and σ54promoters for many of the affected genes and found that greater differences in expression were observed for σ28-controlled genes. Inactivation of the gene encoding σ28,fliA, resulted in an unexpected increase in transcripts with σ54promoters, as well as decreased transcription of σ28-regulated genes. This was unlike the transcription profile observed for the attenuatedC. jejunivariant, suggesting that the reduced virulence of this organism was not entirely due to impaired function of σ28. However, inactivation offlhA, an important component of the flagellar export apparatus, resulted in expression patterns similar to that of the attenuated variant. These findings indicate that the flagellar regulatory system plays an important role in campylobacter pathogenesis and thatflhAis a key element involved in the coordinate regulation of late flagellar genes and of virulence factors inC. jejuni.