Intensive use of parasiticides has sometimes led to severe resistance in arthropods and helminths of veterinary importance. In the context of the growing awareness of parasitic diseases, this has created a public demand for effective and safe control agents. During the last two decades considerable knowledge in parasite neurophysiology and endocrinology has accumulated which allows the development of new screening procedures and target‐site‐directed approaches for the discovery of new drugs. The suitability of this strategic approach is discussed on the basis of recent discoveries of new chemical and natural compounds. In particular, target sites such as GABAA receptors, muscarinic and nicotinic acetylcholine receptors, cuticle synthesis and degradation, ecdysteroid receptors, the calcium release channel and semiochemicals have been selected in order to demonstrate the current approaches to identify new chemical entities, biologically active against nematodes and arthropods.