Imaging by secondary ion mass spectrometry coupled to time-of-flight mass analysis (TOF-SIMS) is a method of which the applications have greatly increased since 10 years. Taking advantage of the development of cluster ion sources, TOF-SIMS offers images of molecular ions at a micrometer lateral resolution or slightly below and does not require complex sample preparation. Although TOF-SIMS has been primarily dedicated to surface analysis of inorganic or polymeric samples, several groups have successfully demonstrated that TOF-SIMS imaging is also perfectly suited for mapping organic compounds, such as drugs or lipids, directly on tissue sections from animals or from human biopsies. This minireview will enlighten some of these developments in the field of biomedical applications.