Studies addressing the functional basis of parasitic manipulation suggest that alteration of the neuromodulatory system is a common feature of manipulated hosts. Screening of the neuromodulatory system has so far been carried out by performing ethopharmacological analysis, biochemical quantification of neurotransmitters and neuromodulators, and/or immunocytochemistry. Here, we review the advantages and limitations of such approaches through the analysis of case studies. We further address whether the analysis of candidate neuromodulatory systems fits the current view of manipulation as being multidimensional. The benefits in combining ethopharmacology with more recent molecular tools to investigate candidate neuromodulatory pathways is also emphasized. We conclude by discussing the value of a multidisciplinary study of parasitic manipulation, combining evolutionary (parasite transmission), behavioural (syndrome of manipulation) and neuroimmunological approaches.