In the decades since its introduction, the neutral theory of evolution has become central to the study of evolution at the molecular level, in part because it provides a way to make strong predictions that can be tested against actual data. The neutral theory holds that most variation at the molecular level does not affect fitness and, therefore, the evolutionary fate of genetic variation is best explained by stochastic processes. This theory also presents a framework for ongoing exploration of two areas of research: biased gene conversion, and the impact of effective population size on the effective neutrality of genetic variants.