Trypanosomatid and apicomplexan parasites remain an important health problem in developing countries. Advances are being made in parts of the world in blocking transmission from insect vectors, but more effective chemotherapy is urgently needed. This is especially important since development of resistance is a growing problem. The rational development of new drugs depends on the identification of differences between human metabolism and that of the parasites. Recent developments in the study of the basic biochemistry of these parasites have resulted in the discovery that bisphosphonates, drugs widely used in the treatment of benign and malignant diseases characterized by increased bone resorption, could have a role as lead antiparasitic agents.