Microsporidia is an obligate intracellular parasite that has been classified under Microspora Phylum, with more than 100 genera and over 1200 species. Microsporidia spp. infecting both vertebrate and invertebrate hosts, cause extracellular infection with their spores. Their size differs according to the species and is often of 1-10 μm. However, the size of Microsporidia spp. infecting mammals is 1.5-3 μm. The first human case due to Microsporidia was reported in 1959. In the last decade interest fort he parasite has increased considerably upon observing that it causses infection in immunocopromised as well as in immunocompetent individuals. For today seven species of Microsporidia are known to infect man: Enterocytozoon, Encephalitozoon, Nosema, Pleistophora, Trachipleistophora, Vittaforma, and Brachiola. Microsporidia can cause infections such as diarrhoea, keratitis, myositis, bronchitis, and bronchiolitis. Besides difficulties occuring diagnosis, The need for special staining methods to detect the parasite, missing the presence of the parasite due to its bacterium-like small size, lack of diagnostic serological methods render the diagnosis of the parasite leading to incomplete epidemiologic data In this paper; the general characteristics, diagnostic methods and difficulties in the diagnosis of Microsporidia spp. are reviewed.