It was during the time he spent working at Frerich's clinic in Berlin that he became interested in the metabolic pathology regarding the liver, pancreas and other internal organs.
With physician Otto Schultzen (1837–1875) he discovered that benzene-derived hydrocarbons in the body had the ability to perform chemistry that was not possible for chemists to achieve in a conventional laboratory.
With pharmacologist Oswald Schmiedeberg (1838–1921) and pathologist Edwin Klebs (1834–1913) he founded Archiv für experimentelle Pathologie und Pharmakologie (now published as Naunyn-Schmiedeberg's Archives of Pharmacology), and in 1896 with surgeon Jan Mikulicz-Radecki (1850–1905) he founded Mitteilungen aus dem Grenzgebieten der Medizin und Chirurgie.
[1] With Oskar Minkowski (1858–1931), he theorized that bile pigment formation was a function of liver cells alone, however this theory was later disproved by John William McNee in 1913.
[4] Frederick Madison Allen described Naunyn as a "champion of strict carbohydrate-free diet in a German medical congress where most of the speakers opposed it".