The use of commercial toxicity prediction systems in a regulatory setting must consider both the limitations and capabilities of the methods, as well as the ultimate use of the predictions, e.g. for testing prioritization, screening, or supporting regulatory decisions. Current systems are better suited to hazard identification (i.e. positive identification of activity-conferring features) than to ruling out hazard. Two recent examples (an EPA testing prioritization exercise for water disinfection byproducts and a regulatory action on 2,4,6-tribromophenol) illustrate issues involved in regulatory applications of SAR and commercial prediction systems. The challenge for the future will be to improve technologies for prediction within the constraints of available data, make optimal use of new test data, and better integrate elements of quantitative modeling (QSAR), empirical association, and biological and chemical mechanisms towards the goal of toxicity prediction.