Milstein was elected a Fellow of the Royal Society (FRS) in 1975, was a fellow of Darwin College, Cambridge from 1980 to 2002, awarded the Louisa Gross Horwitz Prize from Columbia University in 1980, won the Copley Medal in 1989, and became a Companion of Honour in 1995. In 1993 Konex Foundation from Argentina granted him the Diamond Konex Award, one of the most prestigious culture awards in Argentina, as the most important Scientist in the last decade in his country.