[2] His technical work included the Physics Reports review articles Quantum Chromodynamics (with W. Marciano) and "Departures from Chiral Symmetry".

A number of his published papers dealt with the source of the mass of elementary particles in quantum field theory, especially the Nambu–Goldstone realization of chiral symmetry breaking.

He also published (with David Atkatz) a visionary paper entitled "Origin of the Universe as a quantum tunneling event" (1982)[3] that prefigured later work done in the field.

In his capacity as executive director of the New York Academy of Science in 1986, Pagels submitted an affidavit in a case involving a former member of the Transcendental Meditation movement who had sued the organization for fraud.

Heinz Pagels died in 1988 in a mountain climbing accident on Pyramid Peak, a 14,000-foot summit 10 miles to the southwest of the Aspen Center for Physics, where he spent his summers.

As I continued to fall in the dark void, embraced by the vault of the heavens, I sang to the beauty of the stars and made my peace with the darkness.Pagels' work in chaos theory provided the inspiration for the character of Ian Malcolm in Michael Crichton's novel Jurassic Park.