Persistent organic pollutants are widely distributed in the environment and lots of toxicological data are available. However, little is known on the intracellular fate of such compounds. Here a method applying secondary ion mass spectrometry is described that can be used to visualize cellular localization of halogenated compounds and to semi-quantitatively calculate concentrations of such compounds. Of the model compounds tested, TBBPA was homogenously distributed in the cell membrane of the H295R cells while PFOS accumulated in very distinct locations in the cell membrane. Relative intracellular concentrations of 4-OH-BDE69 and 4-OH-BDE121 in GH3.TRE were 61 % and 18 %, respectively, compared to the parent compounds. These differences may partly explain that observed effect concentrations for 4-OH-BDEs in in vitro experiments are usually lower than what would be expected based on receptor binding studies. NanoSIMS50 proved to be a powerful tool to describe the cellular distribution of halogenated compounds. The semi-quantitative data that can be obtained may help to further explain results from in vitro or in vivo experiments.