AimTo investigate the prevalence of metabolic syndrome(MS) in Uighur and Han nationalities (≥50 years) in Xinjiang and compare the differences between the two groups of people.MethodsFrom July 2004 to August 2007,using hierarchical stochastic multistage cluster sampling, field survey and some combined investigation methods, a total of 8,382 people were investigated, including 3,603 Han people (male 1590, 2013 women), 4,779 Uighur people (male 2,347, 2,432 women), and the height, weight and abdominal circumference, blood pressure, blood sugar, blood lipid levels and other related indexes were tested.Results32.85% of Uighur and Han nationality had the prevalence of metabolic syndrome in the middle-aged (male 25.14%, female 39.07%, p<0.05); Han is 27.7% (male 22.53%, female 32.09%, p<0.05); Uighur is 41.03% (male 29.6%, female 50.30%,p<0.05); Uighur is higher than Han (p<0.05 ), and females than males, in which the prevalence of metabolic syndrome in Uighur men and women is higher than that of the Han nationality including both male and female (p<0.05).In two ethnic Uighur woman has the highest prevalence of metabolic syndrome.Prevalence of metabolic syndrome in the different age: from 50~59: Uighur 33.02%, Han 23.59%; from 60~69: Uighur 36.5%, Han 34.44%; above the age of 70: Uighur 27.65%, Han 28.3%.ConclusionsThere are inter-ethnic and gender differences between Han and Uighur in the prevalence of the metabolic syndrome in the middle-aged in Xinjiang.The prevalence of MS is higher in Uighur than in Han, especially in Uighur women.The prevalence of MS is the highest from 60 to 69.