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Approximately one fourth of stroke occur during sleep. Despite the clinical and radiological similarities between wake-up stroke (WUS) and non-WUS, the functional outcomes of WUS are largely unknown.This retrospective analysis reviewed 2289 consecutive patients with acute ischemic stroke who were admitted between November 2002 and December 2009. We used 3 end-point analytic techniques to evaluate the association between WUS and functional outcomes: dichotomized analysis for “functional dependency” (a discharge modified Rankin Scale [mRS] score ≥2 regardless of initial stroke severity), severity-adjusted responder analysis for “unfavorable outcome” (a discharge mRS ≥1 for an admission National Institutes of Health Stroke Scale score 0 to 7; mRS ≥2 for National Institutes of Health Stroke Scale 8 to 14; or mRS ≥3 for National Institutes of Health Stroke Scale ≥15), and shift analysis for changes in overall distributions of discharge mRS scores.The initial National Institutes of Health Stroke Scale score of patients with WUS was significantly higher than that of their non-WUS counterparts (median [interquartile range]; 4 [2 to 7] versus 3 [1 to 6]; P<0.01). The dichotomized analysis strategy failed to detect a significant association between WUS and functional dependency at discharge (adjusted OR, 0.99; 95% CI, 0.76 to 1.28). However, the responder analysis showed that patients with WUS were more likely to have “unfavorable outcomes” (adjusted OR, 1.33; 95% CI, 1.02 to 1.72), and the shift analysis also detected significant effect of WUS on the mRS score distributions toward increased dependency (adjusted OR, 1.22; 95% CI, 1.01 to 1.48).From our study, we documented that WUS was associated with worse short-term outcomes after ischemic stroke. Careful selection of appropriate analytic techniques may help to detect modest associations in observational studies.