After the family moved to Seattle, Perina attended Franklin High School where he graduated as the valedictorian in 1963. He chose the University of Chicago as it offered him full tuition with a stipend. He earned his B.A. degree in history there in 1967 and did his graduate studies at Columbia University where he received his M.A. and Ph.D. degrees in European history, with the idea of going into academia. While studying in New York, he was hired by a film production company to consult and interpret for the filming of a documentary about the 1968 reform movement in Czechoslovakia known as the "Prague Spring". This led to the topic of his Ph.D dissertation: "Intellectuals and Political Change in Czechoslovakia: A History of Literarni noviny and its Contributors, 1952-1969." He had also earned a Foreign Area Fellowship to research his dissertation at the library of Radio Free Europe for two years.