Helicobacter pylori possesses two different flagellin genes, flaA and flaB, which are unlinked on the chromosome and transcribed from sigma(28) and sigma(54) promoters, respectively. Both flagellins are hypothesized to be present in varying amounts in the flagellum, to adapt the physical properties of the flagellar filament to different environmental conditions. The influence of growth phase and environmental conditions on the transcriptional regulation of both flagellin genes has not been investigated so far. Using three different reporter genes as well as Northern blot analyses and RT-PCR, it was determined that both flagellin genes are transcribed in a growth phase-dependent fashion. Growth phase dependency was also found for the flagellar basal body export apparatus gene flhA which is involved in the transcriptional regulation of both flagellin genes. Peak transcription of flaB and flhA occurred earlier during the growth phase than that of flaA, possibly consistent with a hook-proximal localization of the minor flagellin FlaB. Of the reporter gene systems, luciferase fusions reflected best the dynamic regulation patterns of H. pylori flagellin genes. Growth phase in vitro had the strongest influence on transcriptional control of H. pylori flaA and flaB, while differences in supplements to a rich culture medium had only a modest modulatory effect on flagellin gene transcription.