We analyzed 84 Japanese patients with juvenile-onset (before 18 years of age) non-obese diabetes mellitus (DM) for mutations in the genes for HNF-1alpha, HNF-4alpha and HNF-1beta. In HNF-1alpha, previously reported mutations (R271W and R272C) and one novel sequence variant (at nucleotide -129/-130 insTTGGGG of the promoter region) were identified in three different patients. In vitro functional study of the new promoter variant demonstrated that the transcriptional activity was 1.6-2.0 times higher than that of the wild-type. This may lead to overexpression of HNF-1alpha and subsequent negative regulation of the target genes of HNF-1alpha. No mutation was identified in the HNF-4alpha and HNF-1beta genes. In this study on a small series of non-obese Japanese patients with juvenile-onset DM, the prevalence of MODY3 was 3.5%. The significance of the new promoter variant in the development of DM is unclear; however, a promoter mutation in the HNF-1alpha gene could be diabetogenic.