Aims: NanoSIMS (secondary ion mass spectrometry) is a powerful technique for mapping the elemental composition of a variety of small-scale samples (e.g. in Material Research, Cosmochemistry and Geology). However, its analytical features are making it also valuable to address biological questions. We demonstrate the ability of the NanoSIMS 50 to map elements at subcellular lateral resolution (approx. 50 nm) within cyanobacteria (Anabaena sp. and Cylindrospermum alatosporum) and its feasibility to investigate the uptake of bromine-containing substances (NaBr and deltamethrin). Methods and Results: Elemental maps of O, N, P and S were obtained from semi-thin sections of different cell types (chemically fixed and resin-embedded heterocysts, akinetes and vegetative cells). NanoSIMS enabled the detection of various characteristic cell sub-structures and inclusions. A homogenous bromine distribution was detected following NaBr and deltamethrin exposure, at Br-concentrations of 0.05, 0.5 (NaBr) and 0.0025 mmol l(-1) (deltamethrin). Conclusions: NanoSIMS allowed study of the mapping of common elements in cyanobacterial cells and the uptake of NaBr and deltamethrin. Significance and Impact of the Study: These results highlight the potential usefulness of NanoSIMS analysis for tracking elements within cell structures at the nanoscale and the ability to detect marker elements of xenobiotic compounds within exposed organisms.