Objective: Individual differences in macronutrient selection, particularly fat and carbohydrate, and associated body weight gain are partly inherited as polygenic traits, but the potential genetic pathways are unknown. To give an overview of the Quantitative Trait Loci (QTLs) and candidate gene pathways influencing these differences in rat was aimed in this study. Design and Methods: To that end, F2 rats obtained from the crossbreeding between LOU/C and Fischer 344 rat strains to diet self-selection during 3 weeks were submitted. A genome scan was conducted with microsatellite markers covering evenly the whole genome. Genotypes and phenotypes were analyzed separately in male and female F2 rats by multiple interval mapping. Then, lists of candidate genes were treated by the Ingenuity® Pathway software to propose gene pathways involved in our phenotypes. Results: Among numerous others, a QTL on chromosome 12 that influences body weight gain, and fat and carbohydrate choices in the LOU/C x Fischer 344 F2 rat population was found. This locus contains notably the acyl-co-A dehydrogenase gene. Conclusion: A strong genetic determinism and complex pathways involving numerous candidate genes and processes, notably in accordance with the metabolic theory of feeding behavior control were found.