Objective To investigate the prevalence of metabolic syndrome (MS) among Xinjiang Uigur population aged 30-80 and to compare the differences of the three diagnostic criteria used for MS. The three diagnostic criteria were developed by the National Cholesterol Education Program (ATP Ⅲ), International Diabetes Federation (IDF) and Chinese Medical Association Diabetes Branch (CDS). Methods A cross-sectional study was conducted on 2053 Xinjiang Uigur people aged 30-80. The prevalence of MS and the degree of agreement were both calculated according to the three definitions. The results of MS components were also analyzed. Results (1) According to the three definitions (ATP Ⅲ, IDF and CDS), thc prevalence and adjusted prevalence rates of MS were 35.80% (29.64%), 39.41% (35.88%) and 23.72% (19.17%). (2)According to the three definitions (the ATP Ⅲ , IDF and CDS), the prevalence rates of subjects who had at least 3 risk factors were 98.64%, 97.90% and 92.81%. (3) Among all the subjects with MS, the MS diagnostic criteria of ATP Ⅲ and IDF were in good accordance with the Kappa index (0.7801), Youden index (0.7928) and the concordance rate (0.9026). CDS was in relatively weak agreement when comparing with other definitions (ATP Ⅲ and IDF). Conclusion Our findings revealed big differences regarding the prevalence rates, the degree of agreement and the aggregation of risk components on MS among Xinjiang Uigur population. The detection rate of IDF criteria on MS and the highest while detection rate of ATP Ⅲ criteria on subjects presented at least 3 risk factors were the highest. The concordance of ATP Ⅲ criteria and IDF seemed to be a better one.