Insulin promoter factor 1 (IPF-1) is a homeodomain-containing protein that is thought to be a key regulator of pancreatic islet development and insulin gene transcription in beta-cells. This report describes the isolation and characterization of the human IPF-1 gene. The coding region, which showed 83% nucleotide identity with the mouse IPF-1 gene, was encoded by two exons that extended over a 5-kb region of human genome. The deduced human IPF-1 protein contained 283 amino acids, 1 amino acid less than the mouse IPF-1 protein. The homeodomain region of IPF-1 was encoded by the second exon, and it was highly conserved among species. The human IPF-1 gene was mapped to chromosome 13q12(12.1) by fluorescent in situ hybridization (FISH) analysis. A simple sequence repeat polymorphism (ipf1CA2) was identified in the genomic clone. Polymerase chain reaction (PCR) amplification of this repeat region revealed two alleles (heterozygosity = 0.32). This simple sequence repeat polymorphism, and thus the IPF-1 gene, was incorporated into the human linkage map by genotyping reference Human Polymorphism Study Center (CEPH) pedigrees. Multipoint analysis with the CEPH genotype database placed the gene with equal likelihood between two marker intervals: D13S292-cdx3GA1 and cdx3GA1-D13S289 on chromosome 13, consistent with the results of FISH analysis. Two-point linkage analysis inferred that the most likely location for ipf1CA2 was at theta = 0 from cdx3GA1 locus. The exon-intron boundaries of the IPF-1 gene were sequenced, and primers were synthesized to search the homeodomain region for potential variants in patients with NIDDM. By single-strand conformational polymorphism analysis, no variants were found within this region in 61 Japanese patients, which could contribute to the pathogenesis of NIDDM. The isolation of the human IPF-1 gene, along with characterization of its genomic structure and chromosomal mapping, will now permit the assessment of the role of this gene in the pathogenesis of NIDDM in various populations.