The ionome is defined as the mineral nutrient and trace element composition of an organism and represents the inorganic component of cellular and organismal systems. Ionomics, the study of the ionome, involves the quantitative and simultaneous measurement of the elemental composition of living organisms and changes in this composition in response to physiological stimuli, developmental state, and genetic modifications. Ionomics requires the application of high-throughput elemental analysis technologies and their integration with both bioinformatic and genetic tools. Ionomics has the ability to capture information about the functional state of an organism under different conditions, driven by genetic and developmental differences and by biotic and abiotic factors. The relatively high throughput and low cost of ionomic analysis means that it has the potential to provide a powerful approach to not only the functional analysis of the genes and gene networks that directly control the ionome, but also to the more extended gene networks that control developmental and physiological processes that affect the ionome indirectly. In this review we describe the analytical and bioinformatics aspects of ionomics, as well as its application as a functional genomics tool.