Despite numerous studies reporting endophytic fungal production of metabolites chemically similar to the secondary metabolites produced by their host plants, how and why the fungi produce these metabolites remain largely unknown. Here, we review the literature on endophytic fungal production of taxol and camptothecin, two extensively studied plant secondary metabolites, and highlight critical gaps in our knowledge that need to be addressed to adequately answer the above questions. We show that detailed studies are required for conclusive demonstration of i) the production of these metabolites by the fungi, ii) the tolerance of the fungi to the produced cytotoxic metabolites, and iii) the adaptive significance of the metabolite production to the fungi. Although our focus is on two widely studied plant secondary metabolites produced by fungi, the questions addressed here are equally applicable to the production of a large number of other fungal metabolites that are similar to those produced by their host plants.