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The way that immigrants integrate to recipient societies has been discussed for decades, mainly from the perspective of the social sciences. Uruguay, as other American countries, received different waves of European immigrants, although the details of the process of assimilation, when occurred, are unclear. In this study we used genetic markers to understand the process experienced by the Basques, one of the major migration waves that populated Uruguay, and its relation to other immigrants, as well as to Native American and African descendants. For this purpose, we analyze the allele frequencies of ten ALU loci (A25, ACE, APOA1, B65, F13B, PV92, TPA25, HS2.43, and HS4.65) in three samples from Uruguay (two of Basque-descendants, one of non-Basque-descendants) from two locations: Montevideo and Trinidad. No departure from Hardy-Weinberg expectations was observed, with the exceptions of the APO and D1 loci in the non-Basque descendants’ sample. Our data show that the maximum genetic contribution in the three samples comes from Europe (78-88%) with minor African (10-15%) and Native American (0-10%) contributions to the present-day Uruguayan population. Genetic distances reveal that Basque descendants from Trinidad cluster with Europeans, whereas both Montevideo samples cluster together and are separate from other populations, showing two different types of integration, related to the general characteristics of each regional population.