One QTL affecting backfat thickness (BF), intramuscular fat content (IMF) andeye muscle area (MA) was previously localized on porcine chromosome 6 in an F2cross between Iberian and Landrace pigs. This work was done to study the effectof two positional candidate genes on these traits: H-FABP and LEPR genes. TheQTL mapping analysis was repeated with a regression method using genotypes forseven microsatellites and two PCR-RFLPs in the H-FABP and LEPR genes. H-FABP andLEPR genes were located at 85.4 and 107 cM respectively, by linkage analysis.The effects of the candidate gene polymorphisms were analyzed in two ways. Whenan animal model was fitted, both genes showed significant effects on fatnesstraits, the H-FABP polymorphism showed significant effects on IMF and MA, andthe LEPR polymorphism on BF and IMF. But when the candidate gene effect wasincluded in a QTL regression analysis these associations were not observed,suggesting that they must not be the causal mutations responsible for theeffects found. Differences in the results of both analyses showed the inadequacyof the animal model approach for the evaluation of positional candidate genes inpopulations with linkage disequilibrium, when the probabilities of the parentalorigin of the QTL alleles are not included in the model.