OBJECTIVE: The goal of this study was to analyze and differentially diagnose the presence of two large holes noted in the parietal bones of an individual and the presence of traumatic lesions. MATERIALS: A partially mummified young adult female associated with the Chinchorro culture, 4000 BP, from the coast of the Atacama Desert (northern Chile). METHODS: The bone lesions were evaluated macroscopically and radiologically. In addition, Sr isotopic analyses were performed on 62 individuals from eight sites associated with the Chinchorro culture. RESULTS: The parietal orifices are compatible with a rare anomaly of genetic origin known as foramina parietalia permagna (FPP). In addition, the cranial fracture pattern appear compatible with perimortem trauma, and Sr isotopes indicate a marine signal for Chinchorro populations. CONCLUSIONS: This case serves as evidence that FPP was present in the early Andean populations and that endogamy and mutagenic factors might have contributed to its presence. SIGNIFICANCE: This paper expands our knowledge of the genetic anomalies that affected past populations and may contribute to our understanding of the etiologies of the condition. LIMITATIONS: The absence of comparative FPP data inhibits comparative studies (with the exception of cases from California, USA). SUGGESTIONS FOR FUTURE RESEARCH: To explore in depth the genetic component of this condition in the Chinchorro populations.