After completing his service in the IDF in 1960, he studied economics, philosophy and political science at the Hebrew University of Jerusalem. He wrote his PhD on religion and legislation in Israel. After the Six-Day War, he published "War of the Paratroops", and at the beginning of 1973 he published a military history of the early days of Israeli statehood, "By Blood and Fire Judea". In the 1980s, he taught military history at the IDF Command and Staff College. In 1989, Milstein published the first volume of his series on the War of Independence, in which he alleged flawed functioning of commanders who were considered heroes in Israel. Time Magazine assessed it as "the definitive history of the war". Professor Benny Morris of Ben-Gurion University wrote then in The Jerusalem Post and later in Yedioth Ahronoth that until the publication of these books, all that had been written on the war was "a historical smear" and that only from these books is the true story being told. Professor Louis Rene Beres of Purdue University, writing on the books, called them "a strategic asset for the state of Israel".