The most-dominant surface-exposed protein in many bacterial species is the S-protein. This protein crystallises into a regular monolayer on the outside surface of the bacteria: the S-layer. Lactobacillus acidophilus harbours two S-protein-encoding genes, slpA and slpB, only one of which (slpA) is expressed. In this study, we show by polymerase chain reaction (PCR) analysis that slpA and slpB are located on a 6 kb chromosomal segment, in opposite or orientations. In a small fraction of the bacterial population, this segment is inverted. The inversion leads to interchanging of the expressed and silent S-protein-encoding genes, and places the formerly silent gene behind the S-promoter which is located outside the inverted segment. A 26 bp sequence showing a high degree of similarity with the consensus sequence recognized by the Din family of invertases is present in the region where recombination occurs. Expression of the slpA gene seems to be favoured under laboratory growth conditions because 99.7% of the chromosomes of an L. acidophilus ATCC 4356 broth culture had the slpA gene present at the slp expression site.