In this work, the concentration of heavy metals in muscle, liver, fat tissue and skin is studied in 15 Delphinus delphis and two Tursiops truncatus dolphins, stranded along the Portuguese coast of the Atlantic Ocean. Sample collection was performed post-mortem and the tissues were kept frozen until analysed. Sample preparation included lyophilising and grounding in a Teflon mill to avoid contamination by metals. The obtained powder was prepared as pellets for each sample and analysed directly by X-ray fluorescence spectrometry. The concentrations of K, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Rb, Sr, Hg and Pb were obtained. Significant differences between the muscle, the skin and the fat tissues were detected. Cobalt concentrations were similar in liver, skin and muscle. The levels of Ni, Rb and Sr are at the level of the detection limit and whenever measurable are rather constant in all the analysed tissues. The results show that the highest concentrations of Mn, Cu and Hg are always in liver tissues. Zinc and Se concentrations are higher in skin and Pb is present in very low concentrations in all the analysed tissues except in skin; Fe and As are enhanced in muscle and liver. In general, the two studied species did not seem to differ significantly in their heavy metals concentration in a given tissue.