In this paper, we describe both the analytical procedures of isotope ratio measurements and recent progresses in the stable isotope studies of biometals, including iron (Fe) and calcium (Ca). The mass spectrometer utilizing atmospheric pressure plasma ion source (ICP-MS) is the most versatile technique for the stable isotope analysis of heavy elements, and employed in most of the studies. The analytical procedures for minimizing the influence of both mass spectrometric and non-mass spectrometric interferences are quite important for the precise isotopic analysis of Fe and Ca. For Fe isotopes, changes in oxidation states generate large isotopic fractionation through the metabolism of Fe, and the isotope ratio data of Fe can provide information about long-term nutritional status of Fe. For Ca, isotopic ratios of Ca can become a powerful tracer for evaluating the metabolism of Ca in bones. The data presented here revealed that the stable isotope compositions of the biometals can be used as an effective marker for both diagnostics of various diseases related to metabolic disorder and evaluation of nutritional status of both wild and ancient animals.