Protein tyrosine phosphatase-1B negatively regulates leptin and insulin signaling, potentially contributing to hormonal resistance. We selected six tagging single nucleotide polymorphisms (SNPs) representing 18 common variants in the protein tyrosine phosphatase-1B gene (PTPN1) and tested their effect on serum leptin, body fat, and measures of insulin sensitivity and the metabolic syndrome in a large sample of normal female Caucasian twins (n ؍ 2,777; mean age, 47.4 ؎ 12.5 years) from the St. Thomas' U.K. Adult Twin Registry. SNP rs718049 was significantly associated with waist circumference (P ؍ 0.008) and central fat (P ؍ 0.035) and also with Avignon's insulin sensitivity index (SiM) (P ؍ 0.007), fasting insulin (P ؍ 0.004), fasting glucose (P ؍ 0.022), triglyceride (P ؍ 0.023), and systolic blood pressure (P ؍ 0.046). SNPs rs2282146 and rs1885177 were associated with SiM (P ؍ 0.049 and P ؍ 0.013, respectively), and 1484insG was associated with triglyceride (P ؍ 0.029). A risk haplotype (7.3%) was associated with lower SiM (P ؍ 0.036) and a protective haplotype (5.2%) with higher SiM (P ؍ 0.057), with mean values in homozygotes differing by >1 SD (P ؍ 0.003). The protective haplotype also showed lower triglyceride (P ؍ 0.045) and lower systolic blood pressure (P ؍ 0.006). Fine mapping analyses predicted significant associations with SiM and fasting insulin for several ungenotyped SNPs. PTPN1 variants appear to contribute to central fat and metabolic syndrome traits, secondary to their effect on insulin sensitivity. Diabetes 54:3296 -3304, 2005 O besity poses one of the most pressing current public health problems and is a major risk factor for type 2 diabetes. Protein tyrosine phosphatase-1B (PTP-1B) negatively regulates the signaling pathways of insulin and leptin, two hormones involved in the central regulation of energy balance (1). Activated insulin receptor and receptor substrate-1 are dephosphorylated by PTP-1B (2), and phosphorylated JAK2 and STAT3 have been identified as its targets in the leptin pathway (3,4). PTP-1B-deficient mice are hypersensitive to insulin (5) and leptin (4,6) and are protected from diet-induced obesity (4 -6). Hence, increased activity of PTP-1B potentially contributes to leptin resistance associated with overweight (7) and resistance to insulin, which predisposes to type 2 diabetes. In humans, PTPN1, the gene coding for PTP-1B, maps to a region in which a major human quantitative trait locus for obesity and type 2 diabetes has been reported (8 -10). Several rare PTPN1 single nucleotide polymorphisms (SNPs) have been shown to be associated with insulin resistance and diabetes in different populations (11)(12)(13)(14). Recently, Palmer et al. (15) mounted an extensive study of 35 SNPs spanning a 161-kb region including the PTPN1 gene in Ͼ800 Hispanic Americans. Twenty SNPs showed significant association with fasting glucose and the insulin sensitivity index S i . Through its effect on insulin sensitivity, changes in PTP-1B activity may also be refl...