This study was designed to evaluate the epidemiology of type 2 diabetes and hypertension in Uygur and Kazak ethnic populations. A three-step stratified sampling method was used. Questionnaires, blood pressure, anthropometric measurement, and fasting blood glucose were monitored. In total, 1,571 Uygur and 2,913 Kazak subjects were randomly enrolled. The prevalence of type 2 diabetes and glucose intolerance was 5.55- and 1.90-fold higher, respectively, in Uygur than in the Kazak population (8.16 vs. 1.47%, P < 0.001 and 3.29 vs. 1.73%, P < 0.001). However, the prevalence of hypertension and obesity was significantly higher in the Kazak than in the Uygur population (hypertension: 43.52 vs. 31.98%, P < 0.001; obesity: 25.0 vs. 14.5%, P < 0.001, respectively). Our data suggest a significantly different prevalence in hypertension, hyperlipidemia, and type 2 diabetes between the two ethnic groups. The prevalence of type 2 diabetes was much lower, while the prevalence of hypertension was much higher associated with a higher incidence of obesity in the Kazak population. Individuals with a greater BMI and blood pressure were more prone to development of type 2 diabetes. Our data revealed that waist circumference of Kazak ethnics was greater than that of Uygur, even at the same BMI level. Serum fasting glucose was associated with different factors in Uygur and Kazak.