FliH is a soluble component of the flagellar export apparatus that binds to the ATPase FliI, and negatively regulates its activity. The 235-amino-acid FliH dimerizes and interacts with FliI to form a hetero-trimeric (FliH)2FliI complex. In the present work, the importance of different regions of FliH was examined. A set of 24 scanning deletions of 10 amino acids was constructed over the entire FliH sequence, along with several combined deletions of 40 amino acids and truncations of both N- and C-termini. The mutant proteins were examined with respect to (i) complementation; (ii) dominance and multicopy effects; (iii) interaction with wild-type FliH; (iv) interaction with FliI; (v) inhibition of the ATPase activity of FliI; and (vi) interaction with the putative general chaperone FliJ. Analysis of the deletion mutants revealed a clear functional demarcation between the FliH N- and C-terminal regions. The 10-amino-acid deletions throughout most of the N-terminal half of the sequence complemented and were not dominant, whereas those throughout most of the C-terminal half did not complement and were dominant. FliI binding was disrupted by C-terminal deletions from residue 101 onwards, indicating that the C-terminal domain of FliH is essential for interaction with FliI. FliH dimerization was abolished by deletion of residues 101-140 in the centre of the sequence, as were complementation, dominance and interaction with FliI and FliJ. The importance of this region was confirmed by the fact that fragment FliHC2 (residues 99-235) interacted with FliH and FliI, whereas fragment FliHC1 (residues 119-235) did not. FliHC2 formed a relatively unstable complex with FliI and showed biphasic regulation of ATPase activity, suggesting that the FliH N-terminus stabilizes the (FliH)2FliI complex. Several of the N-terminal deletions tested permitted close to normal ATPase activity of FliI. Deletion of the last five residues of FliH caused a fivefold activation of ATPase activity, suggesting that this region of FliH governs a switch between repression and activation of FliI. Deletion of the first 10 residues of FliH abolished complementation, severely reduced its interaction with FliJ and uncoupled its role as a FliI repressor from its other export functions. Based on these data, a model is presented for the domain construction and function of FliH in complex with FliI and FliJ.