Trypanosomatid diseases caused by protozoa belonging to the genera Leishmania and Trypanosomoma represent an increasing global health involving more than 20 million people worldwide. They include leishmaniases, Chagas disease and African sleeping sickness, categorized by WHO as the most challenging neglected tropical diseases (NTDs). Theese pathologies are expanding their frontiers worldwide due to migration phenomenon. Due to the poor interest of big Pharma towards such pathologies new treatment options against these diseases are lacking, while the current chemoteraphy is based on few old drugs endowed with limited efficacy and high toxicity. Thus, the search for new effective agents able to overcome these limits is always a hot topic. To this purpose, a rational approach should rely on metabolic pathways essential for protozoa but absent or sufficiently different in human hosts. Trypanothione reductase (TR) is an attractive target acting as key enzyme in the peculiar redox metabolism of trypanosomatids, being crucial to prevent oxidative damage and allow protozoan survival. Moreover, differently from its human homologue GR, TR displays higher affinity towards positively charged substrates, which relies on different charge distribution in their respective active sites. Recently, we discovered our in-house diaryl sulphide derivative RDS 777 as a promising antiprotozoal compound, being endowed with micromolar inhibitory activities against a panel of clinically relevant parasites and displaying high affinity towards TR of L. Infantum. We solved the X-ray structure of LiTR in complex with RDS 777, highlighting the involvement of several catalytic residues in complex stabilization. This findings gave the basis for a rational design of a new class of TR inhibitors. The data coming from the biological assays will be shown and discussed. A further promising protozoan target is the well known sterol 14-α demethylase (CYP51), a heme-based enzyme that catalyzes the oxidative removal of methyl groups from cyclic sterol precursors leading to ergosterol which is involved in structural and metabolic roles. Depending on parasite species and stages, trypanosomatids show dependence from de novo sterol biosynthesis whose inhibition affect parasitic survival. Ergosterol is also the main sterol in fungi and CYP51 inhibition represents the mechanism of action of currently employed antifungal drugs. Following a drug-repurposing approach, we discovered a series of in-house azole antifungal compounds as potent antiprotozoal agents targeting CYP51. In particular, most of such derivatives displayed optimal nanomolar activities against T. cruzi in in vitro assays. Furthermore, they dramatically reduced parasitemia in T. cruzi mouse model without acute toxicity.