A polymorphic DNA sequence of the apolipoprotein (apo) A-I gene region was studied in relation to non-insulin-dependent diabetes mellitus (NIDDM). We have examined 100 patients with NIDDM and 100 control subjects as well. The presence of a unique 2.5-kilobase (kb) EcoRI fragment was found in 13 diabetic patients and two control subjects with family history of diabetes. There were six homozygotes and nine heterozygotes among them. The analysis of clinical data did not confirm any linkage between the presence of a 2.5-kb fragment and atherosclerosis. These findings suggest that the observed defect in the apo A-I gene region may confer susceptibility to NIDDM.