Background: Obesity prevalence is growing in our population. Twin studies have estimated the heritability of dietary intakes to about 30%. The objective of this study was to verify whether polymorphisms in genes involved in fatty acid metabolism are associated with dietary fat intakes. Methods: Seven hundred participants were recruited. A validated food frequency questionnaire was used to assess dietary intakes. PCR-RFLP and TAQMAN methodology were used to genotype PPARα Leu162Val, PPARγ Pro12Ala, PPARδ –87T>C, PPARGC1α Gly482Ser, FASN Val1483Ile and SREBF1 c.*619C>G. Statistical analyses were executed with SAS statistical package. Results: Carriers of the Ala12 allele of PPARγ Pro12Ala polymorphism had higher intakes of total fat (p = 0.04). For FASN Val1483Ile polymorphism, significant gene-sex interaction effects were found for total fat and saturated fat intakes (p = 0.02 and p = 0.002, respectively). No significant difference in fat intakes was observed for PPARα Leu162Val, PPARδ –87T>C, PPARGC1α Gly482Ser and SREBF1 c.*619C>G polymorphisms. Conclusions: Polymorphisms in PPARγ and FASN seem to be associated with dietary fat intakes. Genetic variants are important to take into account when studying dietary intakes.