To evaluate the risk of site-specific and overall malignancies after SLE and explore the potential influencing factors. We searched electronic databases for articles that assessed the risk of malignancies after SLE through February 2015. We extracted the incidence rates (IRs) and corresponding 95 % confidence intervals (CIs). We used random effects models to calculate the pooled IRs and assessed the impact of study designs, region, gender, age and duration of follow-up. Eighteen studies were included, giving a pooled IR of 1.44 (95 % CI 1.23–1.69). Europeans, Americans and Asians showed a IR of 1.56 (95 % CI 1.07–2.28), 1.18 (95 % CI 1.01–1.39) and 1.62 (95 % CI 1.38–1.89), respectively. Males and females (eight studies) demonstrated a IR of 1.34 (95 % CI 1.07–1.67) and 1.51 (95 % CI 1.20–1.90), respectively. Prospective and retrospective studies showed a IR of 1.55 (95 % CI 0.97–2.47) and 1.44 (95 % CI 1.21–1.73), respectively. An increment of 10 years of age conferred a decrease in IR of 0.6. An increment of 5 years of SLE duration conferred a decrease in IR of 2.5. An increased IR of malignancies was observed in NHL, vagina/vulva, hematology, head/neck, leukemia, thyroid, liver/gallbladder, kidney, anal, cervix, esophagus, lung and pancreas. A decreased IR of malignancies was observed in ovary and colon/rectum. SLE patients had an increased risk of developing overall malignancies, particularly among Asians and females. Age and SLE duration are inversely associated with the risk of overall malignancies. SLE patients showed a different role in the onset of various site-specific malignancies.