Carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the α-, β-, and η-classes are present in many pathogenic protozoa, such as those belonging to the Trypanosoma, Leishmania, and Plasmodium genera. In the last years many such enzymes have been cloned, purified, and extensively characterized. Their inhibition profiles with several classes of CA inhibitors (CAIs) such as the sulfonamides, anions, thiols, hydroxamates, and dithiocarbamates were also investigated. CA inhibition in such protozoa leads to interference with the life cycle of the pathogen, which can be exploited clinically for fighting these widespread infections. However this field is still in its infancy, and these enzymes are attractive yet underexplored drug targets for the management of malaria, Chagas disease, or Leishmaniasis. We also predict that in future years CAs will be characterized in other protozoans, with the possibility to explore alternative drug targets for fighting diseases provoked by them.