East Asia encompasses a wide variety of environments, peoples, cultures and languages. Although this review focuses on East Asia, no geographic region can be considered in isolation in terms of human population history, and migrations to and from East Asia have had a major impact. Here, we review the following topics: the initial colonization of East Asia, the direction of migrations between southeast Asia and northern Asia, the genetic relationships of East Asian hunter-gatherers and the genetic impact of various social practices on East Asian populations. By necessity we focus on insights derived from mitochondrial DNA and/or Y-chromosome data; ongoing and future studies of genome-wide SNP or multi-locus re-sequencing data, combined with the use of simulation, model-based methods to infer demographic parameters, will undoubtedly provide additional insights into the population history of East Asia.