He graduated from the Prague Conservatory, and the Ghent Conservatory, Belgium. He studied under organists Jan Bedrich Krajs and Gabriel Verschraegen. Paukert immigrated to the United States in the 1960s and gained citizenship in 1972.
He taught at several universities, most notably as Professor of Organ and Church Music at Northwestern University and the Cleveland Institute of Music and became curator of the music department at the Cleveland Museum of Art in Cleveland, Ohio. During his tenure at Northwestern in the 1960s and 70's, Paukert was Organist Choirmaster of Saint Luke's Episcopal Church in Evanston, Illinois, and conducted the famed men and boys choir of the church. He founded Bach Week, the annual music festival dedicated to the music of Bach and his contemporaries that has featured leading international performers to this day. He has made recordings for Azica Records.
- St. Paul's Church, Cleveland, Staff List
- Cleveland Artist Award 1995 http://clevelandartsprize.org/awardees/Karel_Paukert.html
- Concert in Prague
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