We present a QTL genome scan for fatty acid composition in pigs. An F2 crossbetween Iberian x Landrace pigs and a regression approach fitting the carcassweight as a covariate for QTL identification was used. Chromosomes (Chrs) 4, 6,8, 10, and 12 showed highly significant effects. The Chr 4 QTL influenced thelinoleic content and both the fatty acid double-bond index and peroxidabilityindex. In Chr 6 we found significant associations with the double-bond index andthe unsaturated index of fatty acids. Chr 8 showed clear effects on thepercentages of palmitic and palmitoleic fatty acids as well as the average chainlength of fatty acids. In Chr 10 we detected a significant QTL for thepercentage of myristic fatty acid, with an F value that was slightly above thegenomewide threshold. The percentage of linolenic fatty acid was affected by aregion on Chr 12. A nearly significant QTL for the content of gadoleic fattyacid was also detected in Chr 12. We also analyzed the genomic QTL distributionby a regression model that fits the backfat thickness as a covariate. Some ofthe QTL that were detected in our analysis could not be detected when the datawere corrected by backfat thickness. This work shows how critical the selectionof a covariate can be in the interpretation of results. This is the first reportof a genome scan detection of QTL directly affecting fatty acid composition inpigs.