Studies in relatively small cohorts provide preliminary evidence that functional fatty acid binding protein 2 (FABP2) promoter haplotypes are associated with type 2 diabetes and BMI. Here, we studied the influence of the haplotypes on BMI by using 8072 male and female participants of the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) cohort. By linear regression analysis, we found in males a reduction of -0.39 BMI units (95% CI: -0.73, -0.05, p = 0.024) in homozygous FABP2 promoter haplotype B carriers. Carriers of haplotype B showed a significant decrease in BMI of -0.19 BMI units (95% CI: -0.35, -0.02, p = 0.027). In accordance, a significant reduction in BMI of the minor haplotype carriers in the BMI point categories of 25-30 (BMI units: -0.10, 95% CI: -0.18, -0.01, p = 0.03) and < 30 (BMI units: -0.37, 95% CI: -0.67, -0.07, p = 0.02) were found. In summary, the minor FABP2 promoter haplotype B contributes to a reduced BMI in men. This provides evidence that functional FABP2 contributes to multifactorialy regulated body weight.