Ganoderma lucidum, an oriental fungus, is widely used for the promotion of health and longevity and is reported to have antioxidant and genoprotective properties. The aim of this study was to investigate the effect of G. lucidum on human lymphocytic DNA ex vivo using the comet assay, and to explore the mechanism of action and the effect of dose. Results showed that G. lucidum has a genoprotective effect at low concentration (0.0001% w/v), but damaged DNA at higher concentrations. The mechanism of damage appeared to be mediated by hydrogen peroxide, which was generated in vitro by G. lucidum, as the effect was ameliorated by the presence of catalase. At concentrations at which no damage was induced, G. lucidum appeared to confer protection against subsequent oxidant challenge to cells. The production of hydrogen peroxide by G. lucidum and its cytotoxic effects should be considered as a factor in future studies. However, the protective effect of G. lucidum at low concentration may explain, in part, some of the reported health benefits of this herb.