Genetic variation of fatty acid binding protein 2 (FABP2) may contribute to the high prevalence of obesity and Type II diabetes in Tonga. To explore this we assessed the frequency of the FABP2 Ala54Thr polymorphism, obesity, and Type II diabetes in Tongans and possible inter-relationships. We investigated 1022 Tongan subjects, 433 men and 589 women aged 15-85 years, to identify possible associations between the FABP2 Ala54Thr polymorphism, obesity, Type II diabetes, BMI, glucose tolerance and standard lipid variables. The prevalence of the polymorphism was compared with that reported for other ethnic populations (studies from: Japanese, Finnish, African American, Native Canadian and Inuit, Swedish, Guadeloupe Indians, European males, and Caucasian populations). We found that 84% of the Tongan men and 93% of the Tongan women were overweight or obese (BMI> or =25kg/m2). The mean BMI+/-SD was not significantly different among those who were and were not carrying the Thr allele (males: Ala/Ala 30.4+/-5.4 and Thr carriers 29.8+/-5.1; females: Ala/Ala 33.8+/-6.4 and Thr carriers 33.6+/-5.1). The genotype frequencies were 76.2% Ala/Ala, 22.8% Ala/Thr, and 1.0% Thr/Thr. The Alal/Ala frequency is higher than the prevalences reported for all populations studied. The Thr allele was significantly associated with lower total cholesterol and LDL cholesterol in both sexes and in women also with lower HDL cholesterol. We conclude that there is a high prevalence of the FABP2 Ala54Thr polymorphism in Tongans. The polymorphism may be involved in lipid metabolism as the Thr allele is associated with low total and LDL cholesterol levels in this population.