Quantitative application of ion beam analysis methods, such as Rutherford backscattering, elastic recoil detection analysis, and nuclear reaction analysis, requires the use of computer simulation codes. The different types of available codes are presented, and their advantages and weaknesses with respect to underlying physics and computing time requirements are discussed. Differences between different codes of the same type are smaller by about one order of magnitude than the uncertainty of basic input data, especially stopping power and cross section data. Even very complex sample structures with elemental concentration variations with depth or laterally varying structures can be simulated quantitatively. Laterally inhomogeneous samples generally result in an ambiguity with depth profiles. The optimization of ion beam analysis measurements is discussed, and available tools are presented.