[citation needed] The institute currently has four departments: Biomolecular Mechanisms (Ilme Schlichting), Chemical Biology (Kai Johnsson), Cellular Biophysics (Joachim Spatz) and Optical Nanoscopy (Stefan W. Hell).

The new, central topic of research is to observe in real time and manipulate the complex dynamics of the interactions between macromolecules in the living cell, in health and disease.

The four departments work in complementary areas: the determination of atomic structures (Ilme Schlichting), optical nanoscopy (Stefan Hell), design of new reporter molecules (Kai Johnson) and cellular material research and biophysics (Joachim Spatz).

The in vivo localization and quantification of protein activities, metabolites and other important parameters has become a central quest in biology, but the majority of cellular processes remain invisible, to date.

The Light microscopy Facility of the Max Planck Institute for Medical Research aims to provide Institute members and guests "low threshold" access to sophisticated microscopy and data analysis equipment, to provide support and training related to sample preparation, data recording and analysis and to stimulate communication and exchange of experience.