Several studies revealed that anthropogenic activities often cause toxic concentrations of some elements, such as mercury, which bio-accumulate through the marine food chain, impacting negatively on the health of animals in the top trophic levels, such as a variety of marine mammals. Moreover, analysis of cetacean skin has been reported to be a reliable, long-term and mostly non-invasive method to monitor bio-accumulation of chemicals in cetacean populations. Several elements, including trace elements, occur naturally in cetacean skin, although nothing is known about their distribution patterns and little about safe base line concentrations. In May 2009, 42 false killer whales (FKWs) beached and died at Kommetjie in the Western Cape of South Africa. Skin samples of these FKWs were collected and analysed to determine elemental distribution patterns. The concentrations and distribution patterns of the major, as well as detectable trace elements were determined in skin samples from ten randomly selected FKW individuals, using micro-PIXE (particle-induced X-ray emission) analysis. Results revealed differences between the distribution patterns of elements in the skin sections. Fe, for example, was found to be concentrated in the dermal papillae, whereas the highest Zn concentrations occurred in the epidermis and particularly in the epidermal papillae. Since these essential elements mediate factors such as host immunity, from skin integrity to humoral immunity, knowledge of their typical distribution patterns can be of great value in studies of bio-accumulation. This is the first report of micro-PIXE being employed to study elemental distribution in cetacean skin and the resulting elemental distribution maps can serve as reference in future environmental pollution studies.