In 2007, based on direct radiocarbon dates, we presented evidence that chickens were introduced to Chile before Europeans first made contact with the New World. The pre-Columbian age of the chicken bones and their mtDNA affinities with one of two prehistoric Pacific chicken haplogroups (E) led us to conclude that Polynesia was the most likely origin for these pre-Columbian chickens. Subsequently, the mtDNA and radiocarbon evidence provided has been applied to a range of studies and occasionally reinterpreted. This has revealed issues related to the brevity of the initial report in 2007. Here, we provide a full discussion of the evidence, including the relevant archaeological, historical and biological information necessary to provide the context for interpreting genetic analyses and understanding their implications for addressing archaeological questions. We include a comprehensive analysis of the isotope data within a geographical and temporally relevant dataset to verify the pre-Columbian age of the El Arenal chickens. In addition, we provide longer DNA sequences obtained from some of the ancient Chilean chicken remains to address objections raised by critics and to demonstrate that longer sequences do not change the observed affinities of the mtDNA sequences, nor their interpretation. In this analysis, historical information is used to critically evaluate the results of phylogenetic analyses. This comprehensive approach demonstrates that the examination of modern chicken DNA sequences does not contribute to our understanding of the origins of Chile's earliest chickens. Interpretations based on poorly sourced and documented modern chicken populations, divorced from the archaeological and historical evidence, do not withstand scrutiny. Instead, this expanded account will confirm the pre-Columbian age of the El Arenal remains and lend support to our original hypothesis that their appearance in South America is most likely due to Polynesian contact with the Americas in prehistory.