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Background: The optimal imaging strategy for selecting candidates for mechanical thrombectomy (MT) remains a matter of debate as its impact on clinical outcome is largely unknown from randomized trials. This study aimed to compare the clinical outcome of MT patients after selection by computed tomography (CT) or magnetic resonance imaging (MRI).Methods: Prospective MT registry data from a large comprehensive stroke center (CSC) was analyzed in anterior circulation LVO patients. Primary endpoint was modified Rankin Scale (mRS, 0-2 vs. 3-6) after 90 days in CT/CTA- (CT group) versus MRI- (MRI group) patients hypothesizing equivalence. Secondary endpoints included workflow times. Subgroup analyses compared directly admitted (mothership) and transferred (drip-and-ship) patients.Results: In 305 MT patients, clinical outcome was not equivalent between imaging groups (odds ratio for mRS 3-6, 0.58 uf05b95% CI, 0.352-0.955uf05d, favoring MRI). A trend towards more favorable outcome in MRI (42.3%) compared to CT group (32.6%; p=0.082) was noted which showed significance in mothership subgroup (48.9% vs. 28%, p=0.023). In hospital workflow times at CSC were equal in mothership patients between CT and MRI groups (door to first angiographic series, 107.5 min versus 109.5 min [p=0.445]; door to recanalization, 148.5 min versus 159 min [p=0.259]). In drip-and-ship patients, second imaging at CSC compared to direct transfer to MT did not change favorable outcome irrespective of utilized imaging modality (p=0.6-0.9).Conclusion: Functional outcome was not equivalent between CT- and MRI-selected MT patients. Overall, MRI selection showed a trend for more favorable outcome which was significant in mothership patients. MRI did not significantly prolong in-hospital workflow.