Numerous scientific investigations have been undertaken to answer the question of Polynesian origins. Most archaeological and linguistic evidence and previous studies in population genetics suggested that Remote Oceania was settled from the west. The human colonization of the Pacific began with the settlement of Australia and Papua New Guinea (PNG) at least 40,000 years ago, and was followed by the settlement of Remote Oceania, starting about 3,500 years ago. Most scholars agree that present-day Polynesians originated in Southeast Asia, and first entered the region as Neolithic agriculturalists. But the questions of the character of colonization and the extent of the Melanesian contribution to the Polynesian gene pool, as well possible South American contacts, still prevail. Certain plants, such as the sweet potato and bottle gourd, indicate some contacts with South America. Moreover, the Norwegian explorer Thor Heyerdahl showed that a voyage from South America was physically possible, even though no direct evidence of Amerindian ancestry has been found. Interestingly, recent research on the HLA system showed a significant South American genetic component in Easter Island. In order to address the issue of possible ancient contacts between Polynesia and South America, and to investigate the genetic affinities of the Eastern Polynesians, 52 human genomic DNA samples from three locations in Eastern Polynesia (Southern Marquesas, Mangareva and Western Samoa) were tested for HLA polymorphisms. The results indicate that the Eastern Polynesians are principally derived from Southeast Asia. Some recent European admixture was detected, most likely due to post-European contacts. Several polymorphisms point to a possible North Asian connection (DRB1*0405 and DRB1*1201) and other, rare elements (e.g. A*0212, B*3905 and DRB1*1402) are clear evidence of South American admixture. No significant Melanesian ancestry was found. Phylogenetic analysis showed that the Polynesians studied did not differ significantly from Southeast Asian populations of mixed origins (such as Malay, Filipino, East Timorese and Moluccans) but have very little in common with the present-day inhabitants of Papua New Guinea. The results, however, could be the effect of sampling variance or genetic drift in Polynesia. In general, the HLA polymorphisms observed in this study give further support to the ‘Express train’ model of the colonization of the Pacific.