Toxicity potentials are scaling factors used in life cycle assessment (LCA) indicating their relative importance in terms of potential toxic impacts. This paper presents the results of an uncertainty assessment of toxicity potentials for 181 substances that were calculated with the global nested multi-media fate, exposure and effects model USES-LCA. The variance in toxicity potentials resulting from choices in the modelling procedure was quantified by means of scenario analysis. A first scenario analysis showed to what extent potential impacts in the relatively short term are obscured by the inclusion of impacts on the very long term. Toxicity potentials representing potential impacts over time horizons of 20, 100 and 500 years were compared with toxicity potentials representing potential impacts over an infinite time horizon. Time horizon dependent differences up to 6.5 orders of magnitude were found for metal toxicity potentials, while for toxicity potentials of organic substances under study, differences remain within 0.5 orders of magnitude. The second scenario analysis addressed to what extent potential impacts on the continental scale are obscured by the inclusion of impacts on the global scale. Exclusion of potential impacts on the global scale changed the toxicity potentials of metals and volatile persistent halogenated organics up to 2.3 orders of magnitude. These scenario analyses also provide the basis for determining exports to future generations and outside the emission area.