During his graduate studies Wüthrich started out working with electron paramagnetic resonance spectroscopy and the subject of his Ph. D thesis was "the catalytic activity of copper compounds in autoxidation reactions". During his time as a postdoc in Berkeley he began working with the newly developed and related technique of nuclear magnetic resonance spectroscopy to study the hydration of metal complexes. When Wüthrich joined the Bell Labs, he was put in charge of one of the first superconducting NMR spectrometers, and started studying the structure and dynamics of proteins. He has pursued this line of research ever since.
After returning to Switzerland, Wüthrich collabrated with among others nobel laureate Richard R. Ernst on developing the first 2 dimensional NMR experiments, and established the nuclear Overhauser effect as a convenient way of measuring distances within proteins. This research later led to the complete assignment of resonances for among others the bovine pancreatic trypsin inhibitor and glucagon.