Genetic assimilation is a process described by Conrad H. Waddington by which a phenotype originally produced in response to an environmental condition, such as exposure to a teratogen, later becomes genetically encoded via artificial selection or natural selection. Despite superficial appearances, this does not require the (Lamarckian) inheritance of acquired characters, although epigenetic inheritance could potentially influence the result. Waddington stated that genetic assimilation overcomes the barrier to selection imposed by what he called canalization of developmental pathways; he supposed that the organism's genetics evolved to ensure that development proceeded in a certain way regardless of normal environmental variations.

The classic example of genetic assimilation was a pair of experiments in 1942 and 1953 by Waddington. He exposed Drosophila fruit fly embryos to ether, producing an extreme change in their phenotype: they developed a double thorax, resembling the effect of the bithorax gene. This is called a homeotic change. Flies which developed halteres (the modified hindwings of true flies, used for balance) with wing-like characteristics were chosen for breeding for 20 generations, by which point the phenotype could be seen without other treatment.

Waddington's explanation has been controversial, and has been accused of being Lamarckian. More recent evidence appears to confirm the existence of genetic assimilation in evolution; in yeast, when a stop codon is lost by mutation, the reading frame is preserved much more often than would be expected.