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Abstract Background Studies have identified high rates of mental disorders in refugees, but most used self-report measures of psychiatric symptoms. In this study, we examined the percentages of adult refugees and asylum seekers meeting diagnostic criteria for major depressive disorder (MDD), post-traumatic stress disorder, bipolar disorder (BPD), and psychosis. Methods A systematic literature search in three databases was conducted. We included studies examining the prevalence of MDD, post-traumatic stress disorder, BPD, and psychosis in adult refugees according to a clinical diagnosis. To estimate the pooled prevalence rates, we performed a meta-analysis using the Meta-prop package in Stata (PROSPERO: CRD42018111778). Results We identified 7048 records and 40 studies (11 053 participants) were included. The estimated pooled prevalence rates were 32% (95% CI 26–39%; I2 = 99%) for MDD, 31% (95% CI 25–38%; I2 = 99.5%) for post-traumatic stress disorder, 5% (95% CI 2–9%; I2 = 97.7%) for BPD, and 1% (95% CI 1–2%; I2 = 0.00%) for psychosis. Subgroup analyses showed significantly higher prevalence rates of MDD in studies conducted in low-middle income countries (47%; 95% CI 38–57%, p = 0.001) than high-income countries studies (28%; 95% CI 22–33%), and in studies which used the Mini-International Neuropsychiatric Interview (37%; 95% CI 28–46% p = 0.05) compared to other diagnostic interviews (26%; 95% CI 20–33%). Studies among convenience samples reported significant (p = 0.001) higher prevalence rates of MDD (35%; 95% CI 23–46%) and PTSD (34%; 95% CI 22–47%) than studies among probability-based samples (MDD: 30%; 95% CI 21–39%; PTSD: 28%; 95% 19–37%). Conclusions This meta-analysis has shown a markedly high prevalence of mental disorders among refugees. Our results underline the devastating effects of war and violence, and the necessity to provide mental health intervention to address mental disorders among refugees. The results should be cautiously interpreted due to the high heterogeneity.