The determinations of trace element and isotopic ratio distributions in rocks and in minerals are key tools for the understanding of geological processes, and they have undergone continuous development for more than 50 years. However, these geochemical tools are not accessible by conventional mineralogical and petrographic in situ methods based on electron or light beams. Therefore, secondary ion mass spectrometry (or ion microprobe) techniques have been used more and more for high-sensitivity in situ analyses at scales down to tens of nanometers. The aim of this paper is to present in the first part the principle of ion probe analysis and the characteristics of the most commonly used ion microprobes today. Then two applications will be presented. The first focuses on the study of alteration processes during hydrothermal alteration of glass. The combination of experiments with isotopically marked fluids and high-resolution in situ isotopic measurements of the marked species allows definition of the main chemical reaction occurring during the alteration. The second example summarizes the contribution of ion microprobe measurements to the understanding of Li and Li-isotope distributions and behaviours in geological processes, and to the determination of Li isotope fractionation during diffusion processes.