This critical review focuses on inductively coupled plasma mass spectrometry (ICP-MS) based applications for isotope abundance ratio measurements in various clinical samples relevant to monitoring occupational or environmental exposure, human provenancing and reconstruction of migration pathways as well as metabolic research. It starts with a brief overview of recent advances in ICP-MS instrumentation, followed by selected examples that cover the fields of accurate analyte quantification using isotope dilution, tracer studies in nutrition and toxicology, and areas relying upon natural or man-made variations in isotope abundance ratios (Pb, Sr, actinides and stable heavy elements). Finally, some suggestions on future developments in the field are provided.