The nuclear microscope is now gaining popularity in the field of life sciences. In particular, the combination of proton-induced X-ray emission to measure the elemental concentrations of inorganic elements, Rutherford backscattering spectrometry to characterize the organic matrix, and scanning transmission ion microscopy to provide information on the density and structure of the sample represents a powerful set of techniques that can be applied simultaneously to the specimen under investigation. These techniques are extremely useful for measuring any imbalances in trace elements in localized regions of biological tissue and, as such, can provide unique information on many diseases. In this article, we describe the nuclear microscope and its related ion-beam techniques, and we review the biomedical work carried out using the nuclear microscope in the National University of Singapore.