Introduction: The mechanisms of early neurological deterioration (END) in patients with acute stroke remain unclear. Despite that systemic hypoxia is associated with stroke risk and poor outcome following acute stroke, the association between nocturnal desaturation and END remains to be elucidated Hypothesis: We assessed the relationship between nocturnal oxygen desaturation in the stroke unit and END in patients with acute stroke. Methods: A consecutive 225 patients with acute ischemic stroke who were admitted to the stroke unit within 7 days after stroke onset between July 2013 and June 2014 were included for analysis Physiological variables including pulse oximetry were sampled every 1 minute. The ODI was calculated using pulse oximetry data during 9 hours on the first night (10:00 PM-7:00 AM) of the stroke unit admission and nocturnal oxygen desaturation was defined as an ODI of 5 or greater per hour. We compared the clinical characteristics, nocturnal oxygen desaturation, laboratory findings, and radiologic findings in patients with and without END. Results: Among the total patients, 52.4 % were male, with a mean age of 66.8 years. Twenty patients experienced early neurological worsening after stroke onset. The proportion of patients with nocturnal desaturation was significantly greater in the group of patients who also showed END (40.0% vs. 9.8%, P < 0.001). Moreover, more patients with END showed poor outcomes at 3 months (65.0% vs. 28.8%, P = 0.001). The stroke lesion locations did not significantly differ between the two groups. After controlling for relevant confounding factors, we found that nocturnal oxygen desaturation was associated with a risk of END (Odds ratio, 5.81; 95% confidence interval, 1.57-21.51). Conclusions: In conclusion, our study found that recurrent nocturnal desaturation in the stroke unit was associated with END in patients with acute stroke. In this context, our data could suggest that intensive monitoring of nocturnal desaturation in the stroke unit could be an important factor in preventing the risk of END and poor outcomes following acute stroke. .