Inbred strains (also called inbred lines, or rarely for animals linear animals) are individuals of a particular species which are nearly identical to each other in genotype due to long inbreeding. A strain is generally defined to be inbred once it has undergone at least 20 generations of brother x sister or offspring x parent mating, at which point at least 98.6% of the loci in an individual of the strain will be homozygous.

Experiments in mice have shown some heterozygosity can still be measured until the 40th generation. Some inbred strains have been bred for over 150 generations, leaving individuals in the population to be isogenic in nature.

Inbred strains of animals are frequently used in laboratories for experiments where for the reproducibility of conclusions all the test animals should be as similar as possible. However, for some experiments, genetic diversity in the test population may be desired. Thus, outbred strains of most laboratory animals are also available, where an outbred strain is a strain of an organism that is effectively wildtype in nature, where there is as little inbreeding as possible.

Certain plants including the genetic model organism Arabidopsis thaliana naturally self-pollinate, which makes it quite easy to create inbred strains in the laboratory (other plants, including important genetic models such as maize require transfer of pollen from one flower to another).

Inbred strains have been extensively used in research. Several Nobel Prizes have been awarded for work that probably could not have been done without inbred strains. This work includes Medawar's research on immune tolerance, Kohler and Milstein's development of monoclonal antibodies, and Doherty and Zinkernagel's studies of the major histocompatibility complex (MHC).

Isogenic organisms have identical, or near identical genotypes. which is true of inbred strains, since they normally have at least 98.6% similarity by generation 20. This exceedingly high uniformity means that fewer individuals are required to produce results with the same level of statistical significance when an inbred line is used in comparison to an outbred line in the same experiment.

Breeding of inbred strains is often towards specific phenotypes of interest such as behavioural traits like alcohol preference or physical traits like aging, or they can be selected for traits that make them easier to use in experiments like being easy to use in transgenic experiments. One of the key strengths of using inbred strains as a model is that strains are readily available for whatever study one is performing and that there are resources such as the Jackson Laboratory, and FlyBase, where one can look up strains with specific phenotypes or genotypes from among inbred lines, recombinant lines, and coisogenic strains. The embryos of lines that are of little interest currently can be frozen and preserved until there is an interest in their unique genotypical or phenotypical traits.

For the analysis of the linkage of quantitative traits, recombinant lines are useful because of their isogenic nature, because the genetic similarity of individuals allows for the replication of a quantitative trait locus analysis. The replication increases the precision of the results from the mapping experiment, and is required for traits such as aging where minor changes in the environment can influence the longevity of an organism, leading to variation in results.