In the fall of 1938, the Iltis family was granted visas to enter the United States thanks to the intercession of the Emergency Committee in Aid of Displaced Foreign Scholars, along with affidavits of endorsement from Albert Einstein and Franz Boas.

In January 1939, when Hitler's military was preparing the invasion of Czechoslovakia, thirteen-year-old Hugo escaped with his mother and his older brother Wilfred on a harrowing train ride that traversed Nazi Germany to France.

He recalled that during a midnight stop at the Stuttgart station, Gestapo officers combed the train, removing ten passengers; the Iltises survived because the boys pretended to be asleep while their mother bluffed that she was the wife of a French diplomat.

In 1955,[4] Iltis relocated to the Botany Department of the University of Wisconsin–Madison, where in addition to directing the herbarium he regularly taught plant geography, taxonomy, and grass systematics.

By the time of his retirement in 1993, he had directed 37 candidates pursuing graduate degrees, and he and his students had collected thousands of specimens throughout the Upper Midwest to document distributions of plant species, leading to the publication of the Atlas of the Wisconsin Prairie and Savanna Flora (2000) coauthored with Herbarium Curator Theodore Cochrane.

[5] One colleague poked fun at Iltis by taping on his office door a cartoon that showed a boss dictating to a secretary and concluding, "Type that up, make ten thousand copies, and send them to all the important people in the world.

He cultivated strong ties with Latin American botanists, often hosting them for extended stays at his home located within the University of Wisconsin–Madison Arboretum.

[8] Iltis used taxonomic and morphological approaches to investigate the domestication of corn, tracing the changes that transformed an unpromising wild grass into one of the most important food crops.

His work supported the view that domestic corn was derived from a species of teosinte, a group of grasses that grows wild in many areas of Mexico.

[5][10] This drawing prompted a Mexican colleague, Luz María Villarreal de Puga (1913–2013), to launch an intensive search for just such a plant, and one of her students, Rafael Guzmán, found it (or so he thought) growing in the wild.

In 1978, Iltis led a team of botanists to the site and determined that it was in fact a heretofore unknown species of teosinte, Zea diploperennis, which is valued for its resistance to certain viruses.

He campaigned with colleagues at the University of Guadalajara to protect the natural environment of Zea diploperennis by creating the 345,000-acre Sierra de Manantlán Biosphere Reserve.

He and his third wife, Sharyn Wisniewski (1950–2013), endowed a fund at the University of Wisconsin–Madison Department of Botany to support graduate student fieldwork in plant systematics.