Purpose To assess changes of retinal vessel oxygen saturation and vessel diameter in healthy individuals during high-altitude exposure. Methods Retinal oxygen saturation and vessel diameter were obtained at sea level (SL, 40 m) and high altitude (HA, 3681 m) on 17 healthy individuals from Beijing (six males, 28.06 +/- 8.06 years) using Oxymap T1 and then compared with 21 residents from Yushu (10 males, 28.63 +/- 6.00 years). Systemic and ocular parameters were also measured before and after high-altitude exposure. Data were presented as mean +/- SD and analysed using paired and independent Student t-test with significance accepted at p < 0.05. Results Short-term high-altitude exposure of Beijing Group significantly affected all the systemic and ocular parameters, as well as retinal oxygen saturation and vessel diameter ranging from overall quadrant to different quadrants, other than retinal venous oxygen saturation and retinal arterial diameter. However, these changes were not evident in those permanently living at HA. Pearson's correlation analysis revealed correlations between retinal oxygen saturation and systemic and ocular parameters (all p < 0.05). The multivariate linear regression analysis indicated that retinal arterial oxygen saturation was significantly associated with arterial peripheral arterial oxygen saturation (SpO(2)) and subfoveal choroidal thickness. Conclusion Short-term exposure to HA induces retinal microcirculation disturbance and auto-regulatory response in healthy individuals, which is probably attributed to arterial SpO(2) and endothelial dysfunction under hypoxic conditions.