Recent studies in rat hepatoma cells identified MAP kinase phosphatase 3 (MKP3) as the key player in antagonizing repression of phosphoenolpyruvate carboxykinase (PEPCK) gene transcription by insulin, indicating that MAP kinase phosphatase can crosstalk with metabolic components of the insulin signaling pathways. The family of histone deacetylases (HDACs) is another set of metabolic therapeutic targets of importance as HDAC1 has recently been shown to be involved in regulating preadipocyte differentiation. We therefore investigated the roles of MKP3 (DUSP6 in human), PEPCK (PCK2), HDAC1&2 single nucleotide polymorphisms (SNPs) in relation to obesity and diabetes risk among 7,287 African American (AA), 3,258 Hispanic American (HA), and 3711 Caucasian American (CA) women participating in the national Women’s Health Initiative (WHI) SNP Health Association Resource (SHARe) and the Genomics and Randomized Trials Network (GARNET). We found significant association between 43 SNPs in the DUSP6 gene region with risk of obesity (risk variants: range of OR=1.08-1.87; protective variants: 0.72-0.93; all P<0.05) and diabetes (risk variants: range of OR=1.08-1.43; protective variants: 0.84-0.93; all P<0.05). Two PCK2 SNPs were associated with obesity risk (risk variant: OR=1.09, P=0.008; protective variant: OR=0.84, P=0.04). Six HDAC2 SNPs were also found to have association with risk of obesity (range of OR: 0.82-0.90, P<0.05) and diabetes (risk variant: OR=1.16; protective variant: 0.77-0.86; all P<0.05). The rs10506969 (C/T) SNP in the DUSP6 gene identified among AA (reference allele=C, OR=0.86, P=0.02) and HA (OR=0.87, P=0.05) was also confirmed in the CARDIoGRAMplusC4D meta-analysis studies of 63,746 coronary artery disease cases and 130,681 controls (reference allele: T, OR=1.05, P=0.003). Our candidate gene study of American women of three ethnicities identified germline mutations in DUSP6, PCK2, and HDAC2 in relation to obesity and diabetes. These human genetic evidence is comparable to data from animal models that support the notion that MAP kinase phosphatase 3, phosphoenolpyruvate carboxykinase, and histone deacetylase 2 may serve as important metabolic therapeutic targets in lowering risk of obesity and diabetes.