Although their history can be traced further back to the study of heredity, variability, and evolution at the beginnings of the 20th century, studies on the genetic structure and ancestry of human populations became important at the end of World War II. From 1950 onward, the tools and practices of human genetics were systematically used to attack global health problems with the support of international health organizations and the founding of local institutions that extended these practices, thus contributing to global knowledge. These developments were not an exception for Mexican physicians and human geneticists in the Cold War years. The first studies, which appeared in the 1940s, reflect the emerging model of human genetics in clinical practice and in scientific research in postwar Mexico. Studies on the distribution of blood groups as well as on variant forms of hemoglobin in indigenous populations paved the way for long-term research programs on the characterization of Mexican indigenous populations. Research groups were formed at the Ministry of Health, the National Commission of Nuclear Energy, and the Mexican Social Security Institute in the 1960s. The key actors in this narrative were Rubén Lisker, Alfonso León de Garay, and Salvador Armendares. They consolidated solid communities in the fields of population and human genetics. For Lisker, the long-term effort to carry out research on indigenous populations in order to provide insights into the biological history of the human species, disease patterns, and biological relationships among populations was of particular interest. Alfonso León de Garay was interested in studying human and Drosophila populations, but in a completely different context, namely at the intersection of studies on nuclear energy and its effects on human populations as a result of World War II, with the life sciences, particularly genetics and radiobiology. In parallel, the study of chromosomes on a large scale using newly experimental techniques introduced by Salvador Armendares in Mexico in 1960 allowed researchers to tackle child malnutrition and health problems caused by Down and Turner syndromes. The history of population studies and genetics during the Cold War in Mexico (1945–1970s) shows how the Mexican human geneticists of the mid-20th century mobilized scientific resources and laboratory practices in the context of international trends marked by WWII, and national priorities owing to the construction movement of postrevolutionary Mexican governments. These research programs were not limited to collaborations between research laboratories but were developed within the institutional and political framework marked at the international level by the postwar period and at the national level by the construction of the modern Mexican state.