In order to evaluate the use of biopsy samples as non-destructive tool for assessing trace element concentrations in small cetaceans, the concentrations of 14 trace elements were determined in skin, blubber, liver and kidneys of four species of small cetaceans (i.e. common dolphin Delphinus delphis, harbour porpoise Phocoena phocoena, bottlenose dolphin Tursiops truncatus and striped dolphin Stenella coeruleolba), stranded and/or by-caught along the NE Atlantic Ocean coast between 2001 and 2008. Only Cu, Fe, Hg, Mn, Ni and Zn were above the detection limit of the instruments and showed recoveries satisfactory enough to be interpreted. Among these trace elements, Hg was the only one showing a significant correlation between concentrations in and those in liver and kidneys. In consequence, skin and blubber can only be used as non-invasive monitoring tissues to investigate Hg bioaccumulation in internal tissues for cetacean populations.