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To assess the paternal history of the Mbya-Guarani Amerindians of northeast Argentina, we examined the genetic variation in seven Ychromosome loci: the binary marker M3 at locus DYS199, and six short tandem repeats (DYS19, DYS389I, DYS389II, DYS390, DYS391, and DYS393). The most striking finding is the high frequency among the Mbya- Guaranı of Q3 lineages with the usually rare alleles DYS391*11 and DYS393*11, which could be the result of a founder effect, given the recent history of the population.