The roles of fimB and fimE in the phase-variable expression of type 1 fimbriae in Escherichia coli were examined. A method was developed to study the effects of fimB and fimE on both recombination of the fim invertible element and fimbrial expression. The method used an allelic exchange procedure consisting of two steps. The first step, construction of intermediate strains, deleted fimB and fimE. This step locked the invertible element in either the on or the off orientation. The second step of the exchange procedure introduced either wild-type or mutant alleles of fimB and/or fimE into the chromosome of the intermediate strains. Analysis of the resulting strains supported the current, plasmid-based model of recombination. Unexpectedly, strains in which the invertible element was locked in the on orientation (either by mutation of both fimB and fimE or, in a control strain, by mutation of the left inverted repeat sequence of the invertible element) continued to exhibit phase-variable expression of type 1 fimbriae. A strain in which fimA was transcribed from the tac promoter continued to exhibit phase-variable fimbrial expression, suggesting that inversion-independent phase variation cannot be explained by variable transcription initiation of fimA.