In-hospital medical complications are common and strongly associated with the risk of death and dependency in stroke patients. Whether similar associations extend to stroke recurrence is unclear. We prospectively and systematically investigated whether in-hospital medical complications are associated with recurrent stroke of patients in the China National Stroke Registry (CNSR). We examined patients with initial ischemic stroke enrolled in CNSR between 2007 and 2008. Recurrent stroke at 3, 6, and 12 months post-stroke was used as stroke outcome. Medical complications were associated with stroke outcomes using multivariable logistic regression.Of the 7593 study patients, recurrent stroke occurred in 1115 (14.7%) within 12 months after stroke onset. In-hospital medical complications were independent risk factors for stroke recurrence in patients with initial ischemic stroke at 3 months (adjusted odds ratio (OR) = 2.19, 95% confidence interval (CI) 1.85 to 2.60), 6 months (adjusted OR = 2.04, 95% CI 1.74 to 2.38), and 12 months (adjusted OR = 1.88; 95% CI 1.62 to 2.19) after onset. The persistence of secondary prevention medications in patients with complications was lower than that in patients without complications.Stroke recurrence post-acute ischemic stroke is significantly associated with in-hospital medical complications.