In the absence of accessible, effective vaccines, the fight against parasitic disease relies mostly on chemotherapy. Nevertheless, the considerable side effects, high costs and growing number of refractory cases comprise substantial drawbacks. Thus, the search for new antiparasitic compounds remains a high priority. The polyamine biosynthesis, conversion and transport pathways offer different targets for selective chemotherapy. Polyamine analogues and other antagonists may provide tools in the search for new lead compounds. Light and electron microscopy techniques may encompass valuable approaches to elucidate the possible mechanisms of action of different antiparasitic compounds, allowing the identification of subcellular target compartments, presumably establishing the basis for a more rational drug design and/or planning of therapeutic strategies.