In recent years the debate regarding possible pre-Columbian introduction of chickens to South America has attracted much attention. A link between ancient Polynesian chickens and those found in a pre-Columbian archaeological site (El Arenal 1) and a modern population (the Mapuche Fowl) in Chile has been proposed based on a shared mtDNA lineage. However, this conclusion has been challenged because the specific lineage (haplotype E1) used to support the genetic connection is found worldwide, and is not specific to Polynesian chickens. Additional evidence of a contemporary Pacific mtDNA chicken profile in an early post-European Peruvian specimen has also been suggested to support pre-Columbian contact. To assess whether modern South American chickens contain ancient Polynesian and/or contemporary Pacific mtDNA profiles, we analysed the mtDNA control region of 229 village and Creole chickens from Chile, Peru, Colombia and Brazil. We compared the results with a dataset of approximately 3,600 sequences of ancient and modern specimens from across the world. Overall, we found that mtDNA profiles in modern South American chickens are related to those found in Asian and European populations, but neither modern Pacific nor ancient Polynesian mtDNA signatures were present in these populations. We will discuss different scenarios to explain these results together with some preliminary analyses of ancient chicken bones from the El Arenal 1 site.