Beginning in the late 1950s, the National Science Foundation and the Rockefeller Foundation sponsored McClintock on research trips to South America and Mexico to study different varieties of maize plants. The Rockefeller Foundation was interested in conducting maize research to engineer better breeds of corn for domestic consumption as part of its political and scientific involvement in Latin America since the late 19th century. Since maize has been an indigenous staple food of civilizations in those regions for thousands of years, studying maize would enable McClintock to test her theories of controlling elements as well as study how maize evolution works on a scale much larger than her experimental plot at Cold Spring Harbor.

Working with graduate students and local scientists in Peru, Colombia, and Mexico, McClintock explored the chromosomal, morphological, and evolutionary characteristics of different races of maize, focusing on analysis of "knobs," that is, the swellings of chromosomal material that occur at positions characteristic of each race. She explained the project in a letter to Curt Stern in February 1960: "I have been working with the maize group in the Rockefeller Foundation in helping to trace the origins of races of maize found in the Americas... I started doing this as a 'contribution' to our Latin American relationships but it is proving to be quite interesting as a piece of research." She also thought that her work might lead to commercial successes in corn breeding.

Beginning in 1962, McClintock supervised four Rockfeller-sponsored scientists who were conducting research projects on Latin American maize at the North Carolina State University in Raleigh. Two of these Rockefeller fellows, Almeiro Blumenschein and Angel Kato, sustained research on Latin American races of maize well into the 1970s. In 1981, Blumenschein, Kato, and McClintock published The Chromosomal Constitution of Races of Maize. It is considered a landmark study that has contributed significantly to the fields of evolutionary botany, ethnobotany, and paleobotany.