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Selenium (Se) is an essential trace element of considerable interest in humans from both a nutritional and a toxicological perspective because of the narrow margin between intakes that result in efficacy and toxicity. It is used as selenocysteine in a few selenoproteins with important physiological functions. Moreover, at supranutritional doses, Se-containing compounds have attracted interest as potential anticancer agents with high efficacy and selectivity against cancer cells. Thus, Se is becoming a widely used dietary supplement. However, accumulating evidence indicate that adverse health effects are associated with excess dietary supplementation. Therefore, characterizing the toxicity of Se metabolic intermediates are important steps to better understand both the beneficial and toxic mechanisms of Se. This review focuses on the metabolism of Se and the biological mechanisms explaining the toxicity of important Se-metabolites in the yeast Saccharomyces cerevisiae, which can be used as a model system to understand the mode of action and the biological effects of supranutritional Se in higher eukaryotes.