Daily nutrition varies considerably among individuals. The number of vegetarians is increasing continuously due to ethical, environmental, religious or other reasons. There is growing concern over their nutritional status with respect to micronutrient deficiencies. Among the essential trace elements, Se is of prime importance as it is part of the active site in selenoproteins. European soil and plants are relatively poor sources of Se, while farm animals are generally supplemented with Se in order to improve their health and avoid deficiency syndromes. We therefore wondered whether German vegetarians display a measurable Se deficiency. To this end, we compared young vegetarians (n 54) and omnivores (n 53). We assessed their Se status by measuring extracellular glutathione peroxidase 3 (GPX3) activity, and concentrations of total serum Se and circulating Se-transport protein selenoprotein P (SEPP). GPX3 activities were not different between the groups, whereas both total Se and SEPP concentrations were reduced to 79·5 and 71·2 % in vegetarians compared with omnivores. When splitting the group of vegetarians into vegans (n 26) and vegetarians consuming egg and milk products (n 28), analyses of the Se-dependent biomarkers did not reveal significant differences. We conclude that low serum Se is mirrored by circulating SEPP concentrations, but not by GPX3 activities in marginally supplied individuals. The specific dietary Se sources, divergent metabolic routes of selenomethionine v. selenocysteine and the different saturation kinetics of GPX3 and SEPP probably underlie our contradictory findings. Whether German vegetarians and vegans need to be considered as a Se-deficient group depends on the biomarker chosen.