Objective To systematically review the differences of selenium levels in environment between endemic and normal regions and in patients with Kaschin-Beck disease and health people. Methods Such databases as PubMed, The Cochrane Library (Issue 8, 2013), EMbase, ISI Web of Knowledge, CNKI, CBM, VIP and WanFang Data were electronically searched to August 16th, 2013 for all observational studies about the differences of selenium levels in environment (including soil, water, and cereal) between endemic and normal regions, and in patients with Kaschin-Beck disease and health people (including blood, urine, and hair) were included. Meta-analysisi was performed using RevMan 5.2 software. Results Forty-six controlled studies were included. The results of meta-analysis showed that, selenium levels in water (SMD= –0.99, 95%CI –1.31 to –0.66), soil (SMD= –1.20, 95%CI –1.92 to –0.49), cereal (SMD= –1.94, 95%CI –2.63 to –1.26) and corn (SMD= –1.66, 95%CI –2.33 to –0.98) in endemic region were lower than those in normal region. The selenium in blood (SMD= –1.03, 95%CI –1.54 to –0.53), blood serum (SMD= –0.66, 95%CI –1.01 to –0.31), red blood cell (SMD= –2.75, 95%CI –4.13 to –1.37), urine (SMD= –0.99, 95%CI –1.43 to –0.55) and hair (SMD= –1.67, 95%CI –2.14 to –1.20) of Kaschin-Beck disease patients were lower than those in healthy people. The results of subgroup analysis also showed that significant differences were found between patients and healthy people in endemic region. The selenium in blood (SMD= –6.12, 95%CI –8.58 to –3.66), blood serum (SMD= –1.02, 95%CI –1.34 to –0.69), red blood cell (SMD= –3.37, 95%CI –5.38 to –1.35), urine (SMD= –1.94, 95%CI –2.54 to –1.34), and hair (SMD –3.49, 95%CI –5.32 to –1.66) of healthy people in endemic region were lower than those in normal region. After removing the specific studies on every pooling outcome with high risk of heterogeneity, the results of sensitivity analysis showed that the results were of robustness and the impact due to heterogenicity was fairly low. Conclusion Selenium levels in external environment in endemic region are significantly lower than those in normal region, and patients’ selenium levels in the body are also significantly lower than the healthy in endemic region. The selenium levels of the healthy in endemic region are also significantly lower than those of the healthy in normal region. Current evidence indicated that lack of selenium in external environment might be related to Kaschin-Beck disease.