Intestinal fatty acid binding protein (I-FABP) participates in the metabolism of fatty acids in the intestinal enterocytes. Threonine encoding allele in codon 54 of the I-FABP gene has been suggested as regulating the absorption of long-chain fatty acids. We examined the fatty acid composition of serum lipid fractions and the concentration of serum free fatty acids after an overnight fast in obese subjects, aged 24-56 years, on their habitual diet. The body mass index of the subjects ranged from 29.7 to 43.3 kg m-2. Six subjects were homozygous for the Thr-54 allele of the I-FABP gene, 37 subjects were heterozygous for the Thr-54/Ala-54 allele and 24 subjects were homozygous for the Ala-54 allele. We did not find any consistent differences in the proportions of long-chain fatty acids in serum triglycerides, cholesterol esters or phospholipids, but the concentration of serum free fatty acids tended to be higher in subjects who were homozygous for the Thr-54 allele (P = 0.13, for trend). In conclusion, our findings suggest that a polymorphism at codon 54 of the I-FABP2 gene does not substantially modify the fatty acid composition of serum lipids in obese Finns.