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Background: Common variable immunodeficiency (CVID) is the most common clinically significant primary immunodeficiency (PID) disorder characterized by variable clinical manifestations including recurrent infections, autoimmune disorders, enteropathy, lymphoproliferative disorders, and malignancy. The aim of this study is to estimate the overall prevalence of malignancy in patients with CVID. Methods: PubMed, Web of Science and Scopus were searched systemically to find eligible studies from the earliest available date to March 2019 with standard keywords. Pooled estimates of the malignancy prevalence and the corresponding 95% confidence intervals (CI) were calculated using random effects models. Results: Forty-eight studies with a total of 8123 CVID patients met the inclusion criteria and were finally included in the meta-analysis. Overall prevalence of malignancy was 8.6% (95% CI: 7.1–10.0; I2 = 79.2%). The prevalence of lymphoma, gastric cancer, and breast cancer in CVID patients were 4.1% (95% CI: 3.3–4.9; I2 = 62.6%), 1.5% (95% CI: 0.78–2.2; I2 = 68.9%), and 1.3% (95% CI: 0.64–1.9; I2 = 54.9%), respectively. Moreover, autoimmunity and malabsorption were more frequent in patients with malignancy than those without malignancy. Conclusion: The prevalence of malignancy has increased in CVID patients due to recent improvement in survival rate and the lymphoma is the most common type. This research highlighted the significance of malignancy screening and management in CVID patients.