Kilstofte's works are characterized by a respect for, and a firm command of, earlier styles and compositional processes; and his work often superimposes creative harmonic structures on lyric lines. Kilstofte has received a number of prestigious compositional awards, including the Rome Prize, the Rudolf Nissim Award, the Goddard Lieberson Fellowship and the Charles Ives Scholarship, the Aaron Copland award (twice), the Francis and William Schuman Fellowship, and the Composers' Award for String Quartet.
His works include orchestral compositions, pieces for band/wind ensemble, chamber works, and choral compositions. The music of Mark Kilstofte is published by the Newmatic Press, Boelke-Bomart, Inc., Gordon V. Thompson Music, Kjos Music Company, Roger Dean Publishing Company, and Equilibrium Recordings. Some of his works have been recorded.