During the interval between the acceptance of Darwinian evolution and the rise of modern understanding of genetics, atavism was used to account for the reappearance in an individual of a trait after several generations of absence. Such an individual was sometimes called a "throwback". The term is often used in connection with the unexpected reappearance of primitive traits in organisms.

The concept was much more widely used in the pre-genetic Darwinism of Ernst Haeckel, who proposed a recapitulation theory commonly summed up in the phrase that ontogeny recapitulates phylogeny: the notion that a developing embryo revisits the previous evolutionary stages of the organism in the course of its development, and resembles the successively more complex organisms out of which it had evolved.

The notion of atavism was used frequently by social darwinists, who claimed that inferior races displayed atavistic traits, and represented more primitive traits than their own race. Both the notion of atavism, and Haeckel's recapitulation theory, are saturated with notions of evolution as progress, as a march towards greater complexity and superior ability.

Ideas that the genetic clock could somehow be reversed led to the selective breeding of cattle with selected primitive traits, in hopes of reviving the extinct aurochs.