Expression of type 1 fimbriae in Escherichia coli is subject to phase-dependent control, with many regulatory inputs from proteins which organise or rearrange the structure of DNA. Inversion of a DNA segment carrying the promoter for expression of fimA, the gene encoding the fimbrial subunit protein, makes a key contribution to the switching of cells between fimbriate and afimbriate states. We have discovered that transcription of fimA is repressed as cells enter stationary phase. This repression is not seen in isogenic strains deficient in rpoS, the gene coding for the stationary phase-specific sigma factor RpoS. RpoS-deficient strains are also altered in the frequency of inversion of the fimA promoter segment. In the strains used in this study, inversion is catalysed by an integrase-like site-specific recombinase encoded by the fimB gene. We report that fimB transcription is repressed strongly as wild-type cells enter stationary phase but that this repression is alleviated in cells deficient in RpoS. These data suggest that RpoS has a negative regulatory role which may be indirect, at both the fimA and the fimB promoters.