To understand the potential toxicity of nanoparticles (NPs), it is necessary to evaluate their penetration in biological tissues. For that, cell imaging can be considered as an indispensable diagnosis method. We have used the NanoSIMS50 to detect particles of a few nanometres diameter unambiguously in biological tissues. Animals (Daphnia magna) or cells were exposed to NPs (titaniumdioxide, silver, silicon oxide and copper oxide). Transmission electronic microscopy (TEM) imaging was used as a complementary technique to secondary ion mass spectrometry (SIMS) imaging. The correlation of SIMS and TEM images opens up a new way of studying the toxicological effects of NPs of interest to medicine and pharmacology.