INTRODUCTION According to palaeoanthropological and archaeological records, East Asia is probably one of the earliest regions settled by our species, Homo sapiens sapiens, after Africa and the Middle East (Lahr and Foley 1994, 1998). Research in this region of the world should thus provide important clues about the history of our species. Moreover, documenting the genetic diversity of East Asian populations is a crucial step in understanding the settlement history of such regions as Japan, insular Southeast Asia and Oceania, as well as the American continent. Continental East Asian populations have recently attracted the attention of molecular anthropologists, as attested by the numerous studies on variation of molecular markers in these populations published during the last four or five years (e.g. Chu et al. 1998; Ding et al. 2000; Karafet et al. 2001; Ke et al. 2001; Oota et al. 2002; Su et al. 1999; Yao et al. 2002a). These studies have provided contradictory results and lead to discrepancies in the interpretation of the genetic history of East Asian populations. There may be several reasons that explain this, including differential or restricted sampling of populations, but most importantly, because each independent component of our genome has its own specific evolutionary history. For instance, gender-specific polymorphisms, such as those studied on the mitochondrial genome and the Y chromosome, have revealed the impact of differential migratory behaviour of men and women on the genetic structure of populations (Oota et al. 2001a; Poloni et al. 1997; Seilestadt et al. 1998). Thus, several polymorphic systems must be analysed to draw more conclusive inferences about the genetic history of populations in East Asia.