Microscopic examination is still considered the gold standard for the diagnosis of parasitic diseases. In many clinical laboratories in hospitals and in health maintenance organizations ("Kupot Holim"), an excellent microscopic identification of parasites is performed. Microscopic examinations using wet mount preparations are performed for the detection of protozoan trophozoites and helmintic ova or larvae. Specific concentration techniques, including flotation and sedimentation procedures are further performed for the diagnosis of parasitic diseases. However, microscopic examinations are time-consuming, non-sensitive and not always reliable. Furthermore, the diagnosis of certain infections is not always possible by searching for the parasites in host tissues or excreta since risky invasive techniques might be necessary to locate the parasites. Detection of antibodies can be very useful as an indication for infection with a specific parasite, especially in individuals with no exposure to the parasite prior to recent travel in a disease-endemic area. In addition to serology, there are other tests of high sensitivity which can be integrated with microscopy, such as antigen detection in stool and blood samples as well as the use of other molecular diagnosis methods. There are two main laboratories in Israel where parasitic diagnosis is available by integration of microscopy, serology, antigen detection and molecular methods: The Reference Laboratory for Parasitology in Jerusalem at the Central Laboratories of the Ministry of Health (MOH) and the Laboratory of Parasitology at Soroka University Medical Center, Beer Sheva (SOR). There are also two special diagnostic units, one responsible for the identification of toxopLasma: Reference Laboratory for Toxoplasmosis, Public Health Laboratory, Ministry of Health, Tel Aviv (Tox), and the other for the identification of Leishmaniasis: Kuvin Center, Faculty of Medicine, Hebrew University of Jerusalem (Kuv). This article summarizes the tests which are currently available for the diagnosis of parasites in Israel and specifies the laboratories in which they can be performed.