Interleukin 1 (IL-1) is selectively cytotoxic to the insulin producing beta cell of pancreatic islets. This effect may be due to IL-1 induced generation of reactive oxygen species and nitric oxide. Since beta cells contain low amounts of the superoxide radical scavenger enzyme manganese superoxide dismutase (MnSOD), this may leave beta cells more susceptible to IL-1 than other cell types. Genetic variation in the MnSOD locus could reflect differences in scavenger potential. We, therefore, studied possible restriction fragment length polymorphisms (RFLPs) of this locus in patients with insulin-dependent diabetes mellitus (IDDM) (n = 154) and control individuals (n = 178). TaqI revealed a double diallelic RFLP in patients as well as in controls. No overall difference in allelic or genotype frequencies were observed between IDDM patients and control individuals (p = 0.11) and no significant association of any particular RFLP pattern with IDDM was found. Structurally polymorphic MnSOD protein variants with altered activities have been reported. If genetic variation results in MnSOD variants with reduced activities, the MnSOD locus may still be a candidate gene for IDDM susceptibility. Whether the RFLPs reported in this study reflects differences in gene expression level, protein level and/or specific activity of the protein is yet to be studied.