In aquaculture, deformities occur in all types of rearing systems, and are always a problem as they reduce the marketing value of fish. Deformities may have numerous origins, among which genetics is usually considered marginal (see review Alfonso, Montero, Rabaina, Astorga, Izquierdo & Gines 2000), although in some cases it appears to be significant (Alfonso et al. 2000; Gjerde, Pante & Baeverfjord 2005). In common carp, deformities also occur under practical conditions, and despite the general knowledge, genetics is often implicated as being a plausible cause by the farmers. One reason for this may be that commercial lines of common carp are often propagated with limited numbers of broodfish, and are often suspected to be quite inbred (e.g. Kohlmann, Gross, Murakaeva & Kersten 2003). In addition, Kirpichnikov (1981) has shown that several fin abnormalities could be attributed to genetics in this species. During the course of a selective breeding experiment on common carp under the semi-intensive pond conditions of Central Europe, we observed the appearance of a significant proportion of deformed fish, and so we decided to investigate the possibility of whether these could be of the genetic origin.