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Controversy exists whether high altitude increases the risk of hypertension (HTN) in permanent inhabitants. Thus, aim was to compare the prevalence of HTN and related factors in residents from different altitude.A stratified multistage random sampling method was used obtain a representative sample of adult residents from below sea-level, 0–1000m, 1000–2000m, 2000–3000m and from 3000–3500m altitude site, Xinjiang China in 2015. Sites were divided into group 1, 2, 3, 4, and group 5. HTN was defined as mean systolic blood pressure (SBP)≥140mmHg, diastolic BP ≥ 90mmHg, and/or on anti-HTN treatment. We compared the prevalence of HTN, related factors and mean BP by different sites.A total of 12477 subjects (50.9% women) were enrolled including 4565 subjects from site 1, 4303 from 2, 1123 from 3, 1117 from 4 and 1369 subjects from site 5. Uygur (94.0%) in site 1, Han (64.5%) in 2, Mongolian and Kazakh (82.0%) in 3, Kyrgyz (99.9%) in 4, and Tajik (97.3%) in site 5 were the major inhabitants. Age-standardized HTN prevalence was the highest in group 3 (20.3%), followed by group 5 and 2 (18.7%; 18.2%) and the lowest in group 4 (8.5%). SBP was the highest in group 3 (126.1 ± 20.4mmHg), and lowest in group 4 (119.8 ± 15.0mmHg). Compared to Han population, higher education attendants, below site 1, those with normal weight, Mongolian (OR = 1.42), Kazakh (OR = 1.46), lower education attainment (OR = 1.55), site 2 (OR = 1.36), overweight (OR = 2.12) and obesity (OR = 3.97) were related to higher HTN prevalence. Results were statistically significant.HTN prevalence and SBP failed to increase in line with elevating altitude in permanent inhabitants. Life styles in ethnic groups, obesity and lower health awareness may be the main contributors of HTN and may be at high priority of health promotion.