The extent and role of mitochondrial DNA damage in the mechanism of action of sulphur mustard (SM) is poorly understood. In this study, a combination of quantitative polymerase chain reaction and Southern hybridization was used to determine the levels of both total DNA adducts and DNA interstrand crosslinks in genomic and mitochondrial DNA isolated from normal human epidermal keratinocytes exposed to SM. The formation of both types of lesions occurred simultaneously in nuclear and mitochondrial DNA, however, SM produced significantly higher levels of both total adducts and crosslinks in genomic DNA than mitochondrial DNA. The total lesion frequency was 0.45 lesions/kb per 100 μM SM in the DHFR gene and 0.12 lesions/kb per 100 μM SM in the mitochondrial segment. Interstrand crosslinks occurred at a frequency of 0.28 crosslinks/10 kb per 100 μM SM in the DHFR gene and 0.05 crosslinks/10 kb per 100 μM SM in the mitochondrial segment. DNA interstrand crosslinks are thought to be the critical lesion produced by similar bi-functional alkylating agents. However, the levels of DNA cross-linking revealed in this study show that even at vesicating doses of SM mitochondrial DNA is still largely free of cross-links and the predominant form of DNA damage contributing to cell death occurs in the nucleus