The major part of Milstein's research career was devoted to studying the structure of antibodies and the mechanism by which antibody diversity is generated. It was as part of this quest that in 1975 he, together with Georges Köhler, developed the hybridoma technique for the production of monoclonal antibodies—a discovery recognised by the award of the 1984 Nobel Prize for Physiology or Medicine. This discovery led to an enormous expansion in the exploitation of antibodies in science and medicine. Milstein himself made many major contributions to improvements and developments in monoclonal antibody technology—especially in the use of monoclonal antibodies to provide markers that allow distinction between different cell types. In collaboration with Claudio Cuello, Milstein helped lay the foundation for the use of monoclonal antibodies as probes for the investigation of the pathological pathways in neurological disorders as well as many other diseases. Milstein and Cuello's work also enabled the use of monoclonal antibodies to enhance the power of immuno-based diagnostic tests. In addition Milstein foresaw the potential wealth of ligand-binding reagents that could result from applying recombinant DNA technology to monoclonal antibodies and inspired the development of the field of antibody engineering which was to lead to safer and more powerful monoclonal antibodies for use as therapeutics. Milstein's early work on antibodies focused on the nature of their diversity at the amino acid level as well as on the disulphide bonds by which they were held together. Part of this work was done in collaboration with his wife, Celia. The emphasis of his research then shifted towards the mRNA encoding antibodies where he was able to provide the first evidence for the existence of a precursor for these secreted polypeptides that contained a signal sequence. The development of the hybridoma technology coupled to advances in nucleic acid sequencing then allowed Milstein to chart the changes that occurred in antibodies following antigen encounter. He demonstrated the importance of somatic hypermutation of immunoglobulin V genes in antibody affinity maturation. In this process, localised mutation of the immunoglobulin genes allows the production of improved antibodies which make a major contribution to protective immunity and immunological memory. Much of his work in recent years was devoted to characterising this mutational process with a view to understanding its mechanism and, indeed, he contributed a manuscript for publication on this topic less than a week before he died. Quite apart from his own achievements, Milstein acted as a guide and inspiration to many in the antibody field as well as devoting himself to assisting science and scientists in less developed countries. It is also worth mentioning, that even though the Nobel Prize would have made him a wealthy man, Milstein did not patent his enormous discovery since he believed that it was mankind's intellectual property. According to his beliefs, his work did not have any economic interest, only scientific.
Milstein married Celia Prilleltensky in 1953. Milstein died early on 24 March 2002 in Cambridge, England at age 74 as a result of a heart condition from which he had suffered for many years. The film "Un fueguito, la historia de César Milstein" was released in 2010, directed by Ana Fraile and awarded Best documentary by the Academy of Film in Argentina.