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Background Direct endoluminal imaging, such as with our previously described microangioscope, is an emerging adjunct in endovascular cerebral aneurysm management that enables clinicians to delineate between thrombi and visualize neoepithelialization after stent placement with high resolution. The present study sought to study flow diversion in vivo under direct endoluminal imaging, and to validate our findings with histopathology. Methods In a rabbit model, we implanted each left common carotid artery with a shielded flow diverter (FD) (Medtronic Pipeline Vantage) and nonshielded FD (Medtronic Pipeline Flex) in the right common carotid artery. We studied 9 animals in 3 groups: (1) no periprocedural antiplatelet therapy, (2) aspirin 81 mg daily, and (3) aspirin 81 mg and clopidogrel 75 mg daily. FD thrombosis, stenosis, malapposition, and neoepithelialization were all evaluated by diagnostic cerebral angiography and microangioscopy after 30 days. Diagnostic cerebral angiography and angioscopic video were analyzed by independent evaluators and compared with histopathologic analysis. Results In the aspirin and dual antiplatelet therapy groups, there were no significant observed differences in stent thrombosis, stenosis, malapposition, or neoepithelialization between the shielded and non‐shielded FD groups. There was significantly more thrombus formation in Group 1. Neointimal thickness as measured by the microangioscope was highly correlated with histology (r = 0.72; P = 0.016). Interrater agreement of microangioscope videos was highest for FD thrombosis and stenosis. Conclusion In‐stent thrombosis, stenosis, malapposition, and neopithelialization demonstrated no significant difference between shielded and non‐shielded FDs. Microangioscopy measurements for neointimal thickness were highly correlated with pathology and may be a helpful adjunct to diagnostic cerebral angiography in FD follow‐up.