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Jean Joseph Clermont Pépin was born in Saint-Georges, Quebec in 1926. Pépin studied with influential Canadian composers Claude Champagne (Montreal) and Arnold Walter (Toronto), and at the Curtis Institute of Music in Philadelphia from 1941 to 1944 with Rosario Scalero. He composed music for a film in 1948. In 1949 he won the Quebec government study grant Prix d'Europe as a pianist, which afforded him the opportunity to study several years in Paris (1949-1955). During this time he studied composition with Arthur Honegger and André Jolivet, and analysis with Olivier Messiaen at the same time as Pierre Boulez, Karlheinz Stockhausen, and Serge Garant.
In the 1950s Pépin's compositions were performed by a number of symphony orchestras. He taught at the Conservatoire de musique du Québec à Montréal from 1955 to 1964 and later served as director from 1967 to 1973.
His pupils included François Dompierre, André Gagnon, André Prévost, Jacques Hétu, Silvio Palmieri and Micheline Coulombe Saint-Marcoux. Pépin was best known for his String Quartets Nos. 3 and 4, his Symphonies Nos. 3 (Quasars), 4 (La messe sur le monde) and 5 (Implosion) and his ballets L'Oiseau-phénix and Le Porte-rêve.
In 1985, he established the Concours de Musique Clermont-Pépin to encourage the development of artists from the Beauce region of Quebec. In 1990, he was named an officer of the National Order of Quebec.
He died of liver cancer in 2006, aged 80.