The goal is to develop molecular systems to support or replace in microscopic characterization and in vitro tests with molecular biology systems capable of improving performance in parasitology tests. In particular, we will analyze the main pathogens: several Leishmania species (Old and New World Leishmania species), the five Plasmodium species of human interest (falciparum, oval, vivax, malariae and knowlesi) and Pneumocistys jiroveci, using molecular methods based on the speed, specificity and sensitivity necessary for their diagnosis. Furthermore, we want to provide specific elements for the typing of the species. Our aim is to improve diagnostic and specie classification methods by using PCR in microbiology and parasitology, to evaluate its impact on diagnosis. We would evaluate the impact of this method in terms of timing, sensitivity and specificity of diagnosis. We would also explore future possibilities on quantification techniques, in order to support the clinician to evaluate the efficacy of therapy during the follow-up. Furthermore, we would evaluate these methods in terms of cost effectiveness towards classical direct methods, which are now operator-dependent.