This study investigated the effects of sedentary occupations on type 2 diabetes and hypertension in different ethnic groups in North West China. All subjects were civil servants who received health examinations in the First Affiliated Hospital of Xinjiang Medical University from October 2010 to March 2014. A total of 46,612 participants (39,120 Han, 4148 Uygur, 2098 Hui, 877 Kazak and 369 other ethnicities) completed the examination. Overall, 16.4% of the Han, 14.4% of the Uygur, 15.9% of the Hui, 20.6% of the Kazak and 16.0% of other ethnicities had hypertension. Diabetes was found in 7.6% of the Han, 8.5% of the Uygur, 9.2% of the Hui, 7.4% of the Kazak, and 3.3% of other ethnicities. There was a significant difference between men and women in the prevalence of diabetes (4.3% in women vs 9.7% in men, p < 0.001) and hypertension (9.7% in women vs 21.0% in men, p < 0.001). Our results indicate that both diabetes and hypertension are highly prevalent in individuals with sedentary occupations.