Segregation distortion is a phenomenon that has been observed in many experimental systems. How segregation distortion among markers arises and its impact on mapping studies are the focus of this work. Segregation distortion of markers can be considered to arise from segregation distortion loci (SDL). I develop a theory of segregation distortion and show that the presence of only a few SDL can cause the entire chromosome to distort from Mendelian segregation. Segregation distortion is detrimental to the power of detecting quantitative trait loci (QTL) with dominance effects, but it is not always a detriment to QTL mapping for additive effects. When segregation distortion of a locus is a random event, the SDL is beneficial to QTL mapping approximately 44% of the time. If SDL are present and ignored, power loss can be substantial. A dense marker map can be used to ameliorate the situation, and if dense marker information is incorporated, power loss is minimal. However, other situations are less benign. A method that can simultaneously map QTL and SDL is discussed, maximizing both use of mapping resources and use by agricultural and evolutionary biologists.