Analytical ion microscopy, a method proposed and developed by R. Castaing and G. Slodzian in Orsay university (France) has been applied to the study of the subcellular distribution of biological molecules and pharmaceutical drugs. This method makes it possible to easily and rapidly obtain analytical images representing the distribution of elements or isotopes in a tissue section (from the three isotopes of hydrogen to transuraniens elements), even when these elements or isotopes are at a trace concentration (1 ppm or less). Recent developments allow to obtain these chemical images at the ultrastructural level. In this paper, images representing the subcellular distribution of halogeneous molecules (pharmaceutical drugs, pyrimidic analogues) and of molecules labeled with a stable isotope are presented.