His neutral theory, formulated in 1968, described rates of evolution and levels of polymorphism solely in terms of mutation and genetic drift (his molecular clock). He concluded that mutations are normally neutral, and more often deleterious than advantageous, but that phenotypic evolution is still due to advantageous mutations. The neutral theory did not deny that natural selection acted on natural populations; but it claimed that the majority of natural variation were transient polymorphisms of neutral alleles. Selection did not act frequently or strongly enough to influence rates of evolution or levels of polymorphism. The neutral theory predicted constancy of DNA change per generation. His theory has come under much opposition by mainstream evolutionists.

This theory was originally published in the magazine Nature under the title Evolutionary rate at the molecular level. He also wrote a book in 1983 The Neutral Theory of Molecular Evolution.