Parasitic diseases constitute the most common infections among the poorest billion people, entailing high mortality rates and leading to long-term infirmities and poverty. Although the setting-up of public health programs implies many ethical consequences, the range of specific questions in parasitology that can be attributed to bioethics remains, to a large extent, unexplored. From the present analysis, it emerged three main issues which characterize ethical stakes in parasitology: accounting the complexity of the field of intervention, putting the principle of justice into practice and managing the changing context of research. From the research angle, medical parasitology-mycology, as other biological disciplines, is undergoing tensions derived from biological reductionism. Thanks to its links with the history and philosophy of the sciences, bioethics can help to clarify them and to explain the growing hold that technologies have over scientific thinking. On the whole, researchers as well as clinicians are called on to assume a specific responsibility, proportional to their competence and their place in the making of scientific, health, economic and social decisions.