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The mummy of a seven-year-old child that was discovered in 1985 in Cerro Aconcagua (Mendoza, Argentina) was likely part of an Inka sacrificial religious practice known as capacocha. Previous uniparental DNA marker studies conducted by some scholars have suggested that the mummified child may be related to the southern Andean population of Peru. However, autosome genome-wide analysis performed by others has indicated that the child was more closely related to the population along the northern Peruvian coast than to that of the southern Andes. In this study, we aimed to determine possible genealogical connections in the male lineage of the mummified child. To achieve this, we compared the genetic profile of the mummy with an extensive database of contemporary individuals from the northern Peruvian coastal and southern Andean regions. We used single nucleotide polymorphisms and short tandem repeats from the nonrecombining region of the Y-chromosome for our analysis. Our results confirmed that the Inka child mummy was closely related to individuals from the north coast of Peru. This suggests that the child was likely descended from the Muchik–Chimor-speaking people.