The first aim of our study was to determine the concentrations of selected trace elements (Zn, Cu, Fe, Mn, Cd and Pb) in tissues of green turtles from Tortuguero National Park on the North Caribbean coast of Costa Rica and of loggerheads from the Mediterranean Sea. Zn, Cu, Fe, Mn and Cd were present at detectable concentrations in all samples and showed clear organotropism, whereas Pb was not always over the detection limit and did not show any particular tissue distribution. The two species presented significant differences: Cu and Cd in liver and kidney of Chelonia mydas were significantly higher with respect to the concentrations found in Caretta caretta. The second and major goal of our study was to evaluate hepatic and renal metallothionein (MT) as a biomarker of environmental metal exposure. The present paper is the first to describe and quantify MT in kidney and liver of loggerhead turtles and in kidney of green turtles. MT concentrations were higher in green than in loggerhead turtles. In addition, positive correlations were found between Cu and Cd concentrations and Cu-MT and Cd-MT in liver and kidney in both species, suggesting a pivotal role of MT in metal storage and detoxification. The quantification of metals and MT in liver and kidney may be a valid biomarker of metal exposure in the aquatic environment to assess the health of marine sea turtles as long as accurate analytical methods are adopted.