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Background:    Although, nontuberculous mycobacteria can cause disease in different organisms, they usually are not reported in most countries because scientists in general consider them as non-pathogens. But, increasing nontuberculous mycobacteria diseases occurrence has changed this belief. Nevertheless, there is no meta-analysis review about prevalence of nontuberculous mycobacteria in Iran.  Methods:   Any data about prevalence of nontuberculous mycobacteria in clinical specimens in Iran were retrieved by searching data bases such as Pub Med, MEDLINE, and Iranian data bases. Then the meta-analysis was performed by comprehensive meta-analysis software (CMA).  Results:    The meta-analysis showed that the prevalence of nontuberculous mycobacteria in the clinical specimens in Iran was 1.3%. In the studies that had sample size less than 300, and in studies conducted after 2004, the prevalence was higher. Also, the prevalence of nontuberculous mycobacteria was higher in the West of Iran. In this study, the most prevalent rapid-growing mycobacterium was Mycobacterium. fortuitum and  most prevalent slow-growing mycobacterium was M. simiae with the prevalence 44.2% and 14.3%, respectively. Conclusion:   M. simiae is the most prevalent nontuberculous mycobacteria in the clinical specimens in Iran. As this species of nontuberculous mycobacteria has similar clinical and radiological manifestations with tuberculosis, it is often treated as tuberculosis. Unfortunately, M. simiae is resistant against first-line anti-TB drugs resulting in treatment failure after using routine anti-TB medication. Therefore, there is an urgent need for application of new diagnostic strategy for identification of nontuberculous mycobacteria species.