Adipose tissue is a key factor determining C-reactive protein (CRP) plasma levels. Variation at the fat-mass and obesity-associated (FTO) gene locus has been reported to be associated with increased body fat. We investigated whether the FTO rs9939609 T>A single nucleotide polymorphism might alter CRP levels in a population-based sample of 2,415 participants from a large prospective cohort study. Genotype/phenotype relationships were studied by linear trend analysis stratified by sex. The rs9939609 A-allele was significantly associated with CRP levels in both genders (men, +21%, P = 0.002; women, +14%, P = 0.01 per A-allele). The association was attenuated, but remained statistically significant after additional adjustment for BMI, waist-to-hip ratio, and other potential confounding factors (men, +14%, P = 0.03; women, +12%, P = 0.02; per A-allele). Similar results were obtained when subjects with CRP levels higher then 10 mg/l were excluded. Our data provide preliminary evidence that the FTO rs9939609 T>A polymorphism contributes to variation in plasma CRP levels independently of obesity indices.