The FABP2 gene variant Ala54Thr has been proposed as an important risk marker for insulin resistance, obesity, diabetes, and metabolic syndrome (MetS). In this study the association of Ala54Thr polymorphism with MetS and its risk components was studied in a local Pakistani population. MetS subjects and controls were recruited from out-patient departments of Pakistani hospitals. Ala54Thr genotyping of 200 MetS patients and 200 healthy controls was performed using a PCR-RFLP. Genotype and allele frequencies were calculated and computed for genetic associations presented as odds ratios (ORs) with a threshold of p≤0.05 to determine statistical significance. The frequency of 54Thr allele of FABP2 significantly associated with MetS risk in Pakistani population. Our results showed that frequency of the FABP2 54Thr allele was significantly higher (67%) in MetS cases as compared to controls (35%)(p<0.0001). The 54Thr allele carriers were at increased risk of MetS (OR=3.93, CI=2.09-7.39, p<0.0001) and obesity (for each SD change in BMI, OR=2.00, CI=1.73-2.32, p<.0001). Our genetic study in a population at risk of MetS highlights the strong association of FABP2 54Thr allele with disease and provides further evidence for the involvement of intestinal fatty acid binding protein in the pathogenesis of MetS.