Objective:To examine all evidences about Microspondia infection in vertebrate/invertebrate hosts and Iranian populations distributed in different regions of the country.Methods:All published articles up to December 2015,including descriptive and cross-sectional studies related to the prevalence and genotyping of Microspondia infection in Iran,was considered in this systematic review.The meta-analysis was done using the random-effects model and Stats Direct statistical software.MEGA 5.05 software and maximum likelihood algorithm with Kimura 2-parameter model were used for phylogenetic analysis.Results:Of the 1 152 investigated studies,33 eligible studies reported a prevalence of Microspondia infection in vertebrate and invertebrate hosts.According to this systematic review,the overall prevalence rate of Microsporidia infection in immunocompromised patients in Iran was 8.18%.Furthermore,the overall prevalence rate of Microsporidia infection in immunocompromised patients with chronic diarrhoea,patients with non-diarrhoea,gastroenteritis,and patients with CD4(< 200 cells/μL) was 15.4%,4.1%,0.5%,and 12.9%respectively.The highest prevalence rate of human and animal Microsporidia was estimated in Kerman(29%) and Khuzestan(26.5%).The overall prevalence rate of Microsporidia infection in honeybees using the random-effects model was 40%.Furthermore,the highest prevalence rate of nosemosis was described in East Azerbaijan(48.2%).The maximum number of Microsporidia isolates from immunocompromised patients and pigeons in Iran belonged to genotypes D(n=16;50%) and E(n=6;20.6%) of Enterocytozoon bieneusi.Conclusions:This study may be the first systematic review and meta-analysis that provides a broad outlook on the prevalence of microsporidiosis in Iran.It is necessary to investigate Microsporidia infection in vertebrate and invertebrate hosts and environmental resources in Iran. Objective: To examine all evidences about Microspondia infection in vertebrate / invertebrate hosts and Iranian populations distributed in different regions of the country. Methods: All published articles up to December 2015, including descriptive and cross-sectional studies related to the prevalence and genotyping of Microspondia infection in Iran, was considered in this systematic review. The meta-analysis was done using the random-effects model and Stats Direct statistical software. MEGA 5.05 software and maximum likelihood algorithm with Kimura 2-parameter model were used for phylogenetic analysis. Results: Of the 1 152 investigated studies, 33 eligible studies reported a prevalence of Microspondia infection in vertebrate and invertebrate hosts.According to this systematic review, the overall prevalence rate of Microsporidia infection in immunocompromised patients in Iran was 8.18% .Furthermore, the overall prevalence rate of Microsporidia infection in immunocompromised patients with chronic diar rhoea, patients with non-diarrhea, gastroenteritis, and patients with CD4 (<200 cells / μL) were 15.4%, 4.1%, 0.5%, and 12.9% respectively.The highest prevalence rate of human and animal Microsporidia was estimated in Kerman ( 29%) and Khuzestan (26.5%). The overall prevalence rate of Microsporidia infection in honeybees using the random-effects model was 40% .Furthermore, the highest prevalence rate of nosmosis was described in East Azerbaijan (48.2%). The maximum number of Microsporidia isolates from immunocompromised patients and pigeons in Iran belonged to genotypes D (n = 16; 50%) and E (n = 6; 20.6%) of Enterocytozoon bieneusi. Confclusions: This study may be the first systematic review and meta-analysis that provides a broad outlook on the prevalence of microsporidiosis in Iran. It is necessary to investigate Microsporidia infection in vertebrate and invertebrate hosts and environmental resources in Iran.