Zeise made several scientific discoveries. His discovery of mercaptans (thiols) in 1832 and thioethers in 1833, was once a weighty support for the influential (now obsolete) "Radical Theory" which Berzelius and Liebig developed, provoking important chemical studies. His discovery and work on xanthates, led to the widespread use of xanthate salts in synthetic chemistry.
In 1830, Zeise attempted to react platinum chloride with ethanol, leading to a series of platinum-based organometallic compounds. One of these compounds, originally referred to by Zeise himself as “sal kalicoplatinicus inflammabilis”, was subsequently named after him according to the tradition of the day &ndash; it is still called Zeises salt. Zeises claim that the newly discovered salt contained ethylene was received with distrust by Justus von Liebig, whose understandable attacks on Zeise were quite unjustified. The complex indeed contains ethylene. Attempts to establish the correct structure and composition of Zeises salt drove much basic research during the second half of the 19th century and led to a greater sophistication in organometallic chemistry. The structure of Zeises salt was definitively resolved only with the advent of X-ray crystallography and the nature of its platinum to ethylene bond was not understood until the development of the Dewar–Chatt–Duncanson model in the 1950s.
Shortly before he died, Zeise published his attempts to purify the pigment carotene from carrot juice while in the Polytechnic Institute; finding it to be soluble in carbon disulfide and correctly identifying it as a hydrocarbon.