Kanatzidis was born in Thessaloniki, Greece. He received his B.S. degree from Aristotle University in 1979 and his Ph.D. from the University of Iowa in 1984 (with Dimitri Coucouvanis). He spent two years at the University of Iowa from 1980 to 1982 and then moved to the University of Michigan when Coucouvanis moved there in 1982.
He was a postdoctoral research fellow at the University of Michigan (1985) and Northwestern University (1986–1987) where he worked with Professor Tobin J. Marks on conductive polymers and intercalation compounds.
He became assistant professor at Michigan State University in 1987. He was promoted to full Professor in 1994. He moved to Northwestern University in 2006.