Domestication of animals has had some important effects on physiology, morphology, behavior and well-being of domesticated animals. Conscious or goal directed selections on animals for increasing their productions has accelerated the rate of the changes, leading to some well-being defections. This paper notes some aspects of animal domestication in context of genetic science. Then explains how domestication may happen, and how does artificial selection alter morphology, physiology and behavior of animals in both useful and harmful ways, with an emphasis on the harmful part. Also correlated responses of selection on domesticated animals are reviewed and some probable solutions to avoid unintended selection are discussed.