He is known for the synthesis and exploration of the properties of graphene-like nanostructures and their potential applications in organic electronics.

He studied chemistry there and was awarded a PhD in 1971 under the supervision of Fabian Gerson at the University of Basel.

He completed post-doctoral studies at the ETH Zurich under Jean François Michel Oth (1926–2003) and received his habilitation in 1977 with a thesis on dynamic NMR spectroscopy and electrochemistry.

Among other things, his group has succeeded in synthesizing and characterizing hitherto unattainable large polycyclic aromatics such as superphenalene, which has a molecular mass of 1182 g·mol−1 and consists of 34 condensed benzene rings.

The graphene-like structures synthesized and investigated by Müllen include two-dimensional bands of less than 50 nanometers width with jagged edges.