The development of molecular biology has made available tools that identify parasites which are important in veterinary parasitology. PCR (polymerase chain reaction) is the most frequently used tool. Target sequences are ribosomal DNA and RNA as well as fragments derived from RAPD (random amplified polymorphic DNA). The most studied protozoan genera have been: Eimeria, Babesia, Theileria, Trypanosoma and Cryptosporidium. Trichinella species and ruminant Trichostrongylid parasites have been the most investigated helminths. The use of molecular tools for identification in veterinary parasitology, however, remains a research technique rather than one that is currently used in the field for diagnostic purposes.