Sequencing of parasite genomes opened the possibity to identify potential protein targets for drug development. Several protein targets have been found in the genome of Plasmodium falciparum, Trypanosoma cruzi, Trypanosoma brucei and Leishmania major. Bioinformatics analysis is an important tool for the identification of protein targets for drug development against parasitic diseases. In this review we comment about three protein targets, identified in parasite genomes, and discuss the main features that may guide future efforts for virtual screening initiatives.