Using the combined techniques of cryoelectron microscopy and image analysis, we generated three-dimensional reconstructions of flagellar filaments from straight, right-handed (SJW1655-R) and straight, left-handed (SJW1660-L) Salmonella typhimurium mutants, both of which have the same parental strain (SJW1103). In the filaments from SJW1655, all flagellin subunits have the same conformation (R), while in filaments from SJW1660, the subunits are all in the alternate (L) conformation. The difference between the two three-dimensional density maps reveal the structural changes that accompany switching of the flagellin subunits between the two conformations. In going from the R to L state, the subunit undergoes a rotation 30 degrees clockwise about a radial axis and 38 degrees clockwise about a vertical axis, and suffers a 50 degrees bend of the outer, relative to the inner, subunit domain. The intersubunit spacing, along the 11-start protofilaments, changes from 51.6 A in the right-handed filament to 52.1 A in the left-handed filament. In order to produce the correct corkscrew shape in native filaments, the change in contacts that produces this shortening of 0.5 A must occur among the inner domains at a radius of about 30 A. We suggest that the changes in the middle domains of the subunit are the switch that forces changes in the inner domains.