As brain size usually increases with body size it has been assumed that the two are tightly constrained and evolutionary studies have therefore often been based on relative brain size (i.e. brain size proportional to body size) rather than absolute brain size. The process of domestication offers an excellent opportunity to disentangle the linkage between body and brain mass due to the extreme selection for increased body mass that has occurred. By breeding an intercross between domestic chicken and their wild progenitor, we address this relationship by simultaneously mapping the genes that control inter-population variation in brain mass and body mass. Loci controlling variation in brain mass and body mass have separate genetic architectures and are therefore not directly constrained. Genetic mapping of brain regions indicates that domestication has led to a larger body mass and to a lesser extent a larger absolute brain mass in chickens, mainly due to enlargement of the cerebellum. Domestication has traditionally been linked to brain mass regression, based on measurements of relative brain mass, which confounds the large body mass augmentation due to domestication. Our results refute this concept in the chicken.Brain size variation across vertebrate species continues to fascinate evolutionary biologists, due in part to the cognitive and behavioral phenotypes it is thought to underlie. Such research is not limited to extant species, with the relationship between brain size and the fossil record capable of identifying the origins and development of avian species, and giving clues as to the evolutionary development of flight 1,2 . Most studies on brain size differences suggest some type of trade-off between the costs of developing and maintaining energetically expensive brain tissue and certain physiological variables (such as body size 3 , metabolic rate 4 and development time 5 ) or lifestyle variables (e.g. foraging ecology 6 and social environment 7 ). One physiological variable that correlates notably with brain size is body size 3 . As brain size usually increases as body size increases 8 it has been assumed that the two are tightly constrained during developmental growth 9 . Researchers have therefore often relied on relative rather than absolute brain size in correlative studies. The relationship between body size and brain size is, however, poorly understood and the use of allometry in brain size evolution studies has been criticized [10][11][12] . Understanding the genetics of brain size evolution is extremely pertinent to determine the relationship between brain size and body size. Most importantly, to what degree is there overlap (and potential pleiotropy) between the genes responsible for both. To date, studies on the genetic relationship between brain and body size are mostly limited to phylogenetic comparisons and measures of selection, and have failed to identify the overlap of the genetic architecture between these traits, especially using a within-species approach. The analysis of the rates of ev...