Total and per gram fecal corticosteroid concentrations were determined for agouti and non-agouti deer mice (Peromyscus maniculatus gracilis) over 24 h under normal caging conditions and after exposure to the stress of novel caging. Per gram corticosteroid concentrations, fecal output, and 24-h corticosteroid production were greater in stressed compared with unstressed deer mice of both color morphs, whereas stressed agoutis had a greater increase in per gram corticosteroid concentrations when compared with non-agoutis. However, due to increased fecal output, stressed non-agouti deer mice had greater 24-h corticosteroid production. Thus, agouti and non-agouti deer mice differ in their hormonal reaction to stress. This is the first demonstration of corticosteroid differences associated with the agouti locus.