Two restriction fragment length polymorphisms (RFLPs) near the human islet amyloid polypeptide (IAPP) gene were examined in 50 Japanese patients with non-insulin-independent diabetes mellitus (NIDDM) and 54 non-diabetic controls. RFLPs were identified with the enzymes PvuII (A1 = 21 kb and A2 = 18 kb) and BglII (B1 = 9 kb and B2 = 7 kb). These RFLPs were in complete linkage disequilibrium with A1 which was in disequilibrium with B2, as was A2 with B1. Since these two RFLPs map to different locations in the 5'-flanking region of the IAPP gene, they are most likely due to changes in the sequence of the sites recognized by PvuII and BglII rather than to an insertion/deletion-type DNA polymorphism. There were no differences in the genotypic or allelic frequencies of these RFLPs between Japanese subjects with NIDDM and non-diabetic controls implying that these RFLPs do not play a major role in the development of NIDDM in this population.