We found a novel G-->A change at nucleotide -25 within the promoter of the CTSS gene encoding the elastase cathepsin S. The CTSS -25G/A polymorphism could be detected by digestion with endonuclease BfmI. The frequency of the CTSS -25A allele was 0.457 in Caucasians and 0.431 in Canadian Inuit. Because of the importance of the CTSS gene product in vascular matrix remodeling, this polymorphism may be useful in the study of associations with atherosclerosis and related phenotypes.