Leopard seal, Hydrurga leptonyx, and Weddell seal, Leptonychotes weddellii, occupy an upper trophic level within the Antarctic ecosystem and are useful indicator species in the Southern Ocean of trace element concentrations. Reference values for the concentration of 19 trace elements were determined in the serum and hair of leopard and Weddell seals sampled in Eastern Antarctica. These reference values can be used as 'baseline' levels for monitoring trace element concentrations in these species. Greater trace element concentrations were determined in hair compared to serum, indicating different time scales of trace element accumulation in these samples. For the majority of trace elements, except for Se in the leopard seal samples and Cr in the Weddell seal samples, significant regression relationships for trace element concentrations in hair and serum were not elucidated. Significant differences were determined in the concentrations of seven out of 15 elements with hair type, moult and new, in the leopard seal; concentrations in moult hair were determined to be greater than in new hair for all elements except Zn. Hair analysis was determined to be useful for monitoring exposure to trace elements and when collected off the ice from moulting seals, hair can be employed as a non-invasive sample for trace element analysis in leopard and Weddell seals.