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β-Lapachone (β-lap) is a promising antitumour drug currently undergoing clinical trials. Although it is known that β-lap generates reactive oxygen species (ROS), its actual mechanism of action is still controversial. Especially important is to determine whether concomitant DNA or microtubule damage is the key target of its antitumour properties and whether DNA damage is mediated by topoisomerases as previously suggested. Here, we have searched for determinants of β-lap cytotoxicity in the model organism Saccharomyces cerevisiae through a mechanism-driven approach whereby several pathways of the DNA and microtubule integrity responses, as well as the anti-oxidant response, were downregulated and the outcome of β-lap treatment examined. We also included in the analysis several β-lap derivatives expected to modify drug bioavailability and activity. We found that neither topoisomerase II nor microtubules contributed to yeast sensitivity to β-lap and its equitoxic derivative 3-bromo-β-lapachone. Instead, we found that oxidative and related environmental stresses were primarily responsible for toxicity. Accordingly, Yap1, the central transcription factor in the antioxidant response in yeast, together with several components involved in stress tolerance (i.e., Snf1 and Hog1) and chromatin remodelling (i.e., the SWR1 and RSC complexes), played major roles in protection against β-lapachone. Critically, we show that dioxygen enhanced toxicity and that ROS scavengers protected cells from it. Furthermore, we show that both quinones resulted in cell death in a manner which cytologically resembled apoptosis/necrosis. We thus conclude that β-lap is toxic to yeast through massive ROS production that either directly kills the cells or else triggers programmed cell death.