Chronic kidney disease is a significant public health problem worldwide. However, the causes of chronic kidney disease in Iran are unclear. This systematic review and meta-analysis identified the causes of chronic kidney disease in the general population of Iran. International databases (PubMed, Web of Science, Scopus, and Google Scholar) and national databases (Scientific Information Database and Magiran) were searched for studies published until March 1, 2018. The quality of the studies was assessed using the checklist developed by Hoy et al. Of 2518 retrieved studies, 26 studies involving 34,683 patients with chronic kidney disease stages 1 to 5 were included in the meta-analysis. The mean age of the cohort was 53.6±15.02 years. The results of the random-effects model showed that the three leading causes of chronic kidney disease were diabetes, hypertension, and glomerulonephritis, with an overall prevalence of 27.7%, 27.6%, and 6.4%, respectively. These results indicate the importance of addressing these risk factors at the national level to reduce disease prevalence.