A subgroup analysis of access site complications in the Japanese Registry of Neuroendovascular Therapy (JR-NET) and JR-NET2, which were retrospective registry studies, was performed. Puncture site vascular complications occurred in 195 (0.63%, mean age: 69.2) of all 31,836 patients. Most of these complications resulted from surgery in main hospitals (186 patients, 0.67%, P < 0.001) and scheduled surgery (167 patients, 0.73%, P < 0.001). Carotid artery stenting (81 patients, 1.04%, p < 0.001), extracranial percutaneous transluminal angioplasty (PTA) (15 patients, 1.02%, p < 0.001), and intracranial PTA (10 patients, 0.81%, p < 0.05) were associated with significantly higher incidence of complications. The incidence of puncture site vascular complications was correlated with the number of antiplatelet drugs (p < 0.001) and intraoperative heparinization (p < 0.05).