Increased production has been the major goal of animal breeding for many decades, and the correlated side-effects have grown tobecome a major issue in animal welfare. In this paper, the main genetic mechanisms in which such side-effects may occur arereviewed with examples from our own research in chickens. Pleiotropy, linkage and regulatory pathways are the most importantmeans by which a number of traits may be affected simultaneously by the same selection pressure. Pleiotropy can be exemplified bythe gene PMEL17 which causes a lack of black pigmentation in chickens and, simultaneously, predisposes them to become the victimsof feather pecking. Linkage is a probable reason why a limited region on chicken chromosome 1 affects many different traits, suchas growth, reproduction and fear-related behaviour. Gene regulation is affected by stress, and may cause modifications in behaviourand phenotype which are transferred from parents to offspring by means of epigenetic modifications. Insights into phenomena, suchas these, may increase our understanding not only of how artificial selection works, but also evolution at large.