Ultrastructural immunocytochemistry, using antisera raised against specific subunits of glutathione S-transferases, indicated differences in the intracellular compartmentalization of these enzymes in the bronchiolar epithelia of rats and mice. Antisera raised against subunits of the alpha-class derived from both rats (Ya) and mice (Yc) labeled secretory granules in Clara cells of rats, but not mice, and they also labeled mitochondria throughout murine bronchioles. In contrast, antiserum to a mu-class subunit derived from rats (Yb-1) did not result in any labeling over the Clara cell granules of rats but produced intense labeling over those of mice. Antiserum raised against a rat-derived pi-class subunit (Yp) did not label Clara cell granules or mitochondria in either rats or mice but produced a slight concentration of label over the nuclei of murine cells. Variations in the distribution of glutathione S-transferases may contribute to interspecies differences in the sensitivity of particular lung cells to toxins. Isoenzymes of glutathione S-transferase, secreted into the bronchioles of rats and mice, may help to protect the epithelium from extracellular toxins.