Born in Sulzbach, Kaunzinger studied organ, piano, conducting and composition in Nuremberg and Frankfurt (Main), where he also worked as a coach at the Opera.
[1] From 1968 to 1974 he studied organ in Paris with Marie-Claire Alain, Maurice Duruflé and Jean Guillou.
In 1976, he was appointed both head of the organ department at the Catholic University of America and "artist in residence" at the National Shrine of the Immaculate Conception in Washington, D.C.[3] He returned to his position in Würzburg in 1978.
He conceived the organ of the Stiftsbasilika Waldsassen, built by Georg Jann with 6 manuals and 103 stops.
He founded the "Memminger Meisterkurse für Orgelinterpretation" (Memmingen masterclasses for organ interpretation), with an emphasis on French romanticism.