In Escherichia coli the flagellar regulon consists of more than 60 genes organized in three hierarchically and temporally regulated transcriptional classes. The flagellar sigma factor FliA (sigma(28)) is responsible for class 3 expression and, in the early phase of flagellar assembly, is inhibited by its anti-sigma factor FlgM. The flagellar hook basal body forms a type III secretion system capable of secreting both flagellar subunits and FlgM. This results in release and therefore activation of FliA and class 3 expression. Here we demonstrate that FliA is also subject to proteolysis which mainly depends on Lon protease. FlgM not only acts as an anti-sigma factor but also protects FliA from being degraded. Based on quantitative measurements over time upon experimental induction of the flagellar cascade as well as during the growth cycle of a motile strain, we show that FliA proteolysis increases in parallel to class 3 expression, i.e. correlates with FlgM secretion and the phase of highest activity of FliA. Thus, when FlgM is not available due to secretion or mutation, and with RNA polymerase interaction being only transient during the transcription initiation cycle, the proteases can degrade FliA. Experiments with a lon mutant indicate that Lon protease and FliA degradation maintain appropriate FliA : FlgM stoichiometry upon induction of the flagellar system and thereby contribute to timely shut-off of this system.