He entered Penn medical school in the Fall of 1960, but discovered that he was more interested in research, particularly after spending the summer of 1962 carrying out research on protein biosynthesis under the supervision of Sydney Brenner at the Laboratory of Molecular Biology, Cambridge, England.

He decided to pursue a Ph.D. and became one of Penn's first M.D.-Ph.D. students, working with Robin Hochstrasser on molecular spectroscopy of single crystals of heme proteins.

[3] Eaton has spent his entire career at the NIH after arriving as a medical officer in the Public Health Service in January 1968, leaving only once for a significant period of time to teach physical chemistry as a visiting professor at Harvard for the Spring semester of 1976.

[3] In addition to research, Eaton is credited for developing the Laboratory of Chemical Physics within the National Institute of Diabetes and Digestive and Kidney Diseases, NIH into one of the very top biophysics/structural biology departments in the USA.

Eaton, as Chief of the Laboratory of Chemical Physics, recruited the legendary theorist, Robert Zwanzig, and scientists such as Ad Bax, Marius Clore FRS, Angela Gronenborn, Attila Szabo, and Robert Tycko all of whom were subsequently elected to the US National Academy of Sciences.