Most of Johnston's later works use a large number of pitches, generated through just-intonation procedures. In these works, he forms melodies based on an "otonal" eight-note just-intonation scale made from the 8th through 15th partials of the harmonic series, or its "utonal" inversion. He then gains new pitches by using common-tone transpositions or inversions. Many of his works also feature an expansive use of just intonation, using high prime limits. His String Quartet No. 9 uses intervals of the harmonic series as high as the 31st partial. He uses "potentially hundreds of pitches per octave," in way that is "radical without being avant-garde," and not for the creation of "as-yet-unheard dissonances," but in order to, "return... to a kind of musical beauty," he perceives as diminished in Western music since the adoption of equal-temperament. "By the beginning of the 1980s he could say of his elaborately microtonal "String Quartet no. 5"... 'I have no idea as to how many different pitches it used per octave'".