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Fish are widely used in numerous fields of basic and applied research. Currently, they are the third laboratory animal group in numbers, and will become increasingly important. Common carp is a major species in both aquaculture and research. Inbred strains of carp by gynogenetic (only female inheritance) and androgenetic (only male inheritance) reproduction techniques were developed at our university. With these methods, homozygous animals are produced in one generation and we present the production of homozygous inbred and F1 hybrid strains of common carp. As in mammalian research, using genetically well defined fish is a methodological necessity since in outbred stocks: (1) repeatability between experiments is low, (2) high levels of inbreeding may have accumulated and (3) high intrastrain variability might obscure treatment effects. Within inbred strains, the variation is reduced and as a result, less animals (compared to outbreds) are necessary to obtain statistically significant results. We illustrate this with experimental data from an F1 hybrid and partly outbred strain of common carp, both subjected to an antibiotic treatment resulting in reduced gonadal growth. Results obtained from a single inbred strain should be generalized with the use of a panel of inbred strains. We show that optimal allocation of animals between and within inbred strains depends on the ratio (variation between strains): (variation within strains). When selecting a panel of inbred strains, attention has to be paid to genetic relations between strains to avoid testing within a limited genetic range. It should be considered that in inbred strains, (genic) dominance and interaction effects are absent, due to the absence of heterozygous genotypes. In general, variation within inbred strains will be reduced for traits with a high degree of genetic determination. However, in inbred strains of carp produced by gynogenesis or androgenesis, the chromosome manipulation treatment induces considerable (environmental) variation. By using F1 hybrids of carp, derived from crossing homozygous clonal siblings this source of variation can be avoided. Still, variation in F1 hybrids of carp is relatively large and varies greatly between strains when compared to inbred strains of laboratory rodents. It is assumed that their poikilothermic nature makes them more susceptible to environmental variation. Using inbred fish lines will increase experimental quality and leads to a more efficient use of experimental animals.