The transition metals Fe, Cu and Zn are the key elements for life, and their isotope compositions are expected to be a new index to diagnose human diseases. This article reviewed the principle of Fe, Cu and Zn isotopes in medicine, and the research of their application in medical diagnosis. Because Fe isotopes can effectively trace the diseases related to Fe metabolism, Cu isotopes plays an important role in tracing liver disease and cancer, and Zn isotopes can be used as an effective tracer for cancer in secretory organs, these isotopes can be used in medical diagnosis. We hope this study will promote the research and application of metal stable isotopes in medicine and establish the index of metal stable isotope in medical diagnosis.