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Objective We performed a retrospective observational study to demonstrate the surgical risks and long-term prognoses of intramedullary tumors in Japan using a multicenter registry authorized by the Neurospinal Society of Japan. Methods Data from 1,033 consecutive patients with intramedullary tumors, treated between 2009 and 2020, were collected from 58 centers. Patients with spinal lipomas or myxopapillary ependymomas were excluded. Patient characteristics, clinical presentations, imaging characteristics, treatments, and outcomes were analyzed. The modified McCormick scale was used to classify functional status. Survival was described using Kaplan-Meier curves, and multivariable logistic regression analyses were performed. Results The mean age of the patients was 48.4 years. Data of 361 ependymomas, 196 hemangioblastomas, 168 astrocytic tumors, 160 cavernous malformations, and the remaining 126 cases including subependymomas, metastases, schwannomas, capillary hemangiomas, and intravascular B-cell lymphomas were analyzed. Twenty-two patients were undiagnosed. The mean follow-up duration was 46.1 ± 38.5 months. Gross total tumor removal was achieved in 672 tumors (65.1%). On the modified McCormick scale, 234 patients (22.7%) had worse postoperative grades at the time of discharge. However, neurological status gradually improved. At 6 months postoperatively, 251 (27.5%), 500 (54.9%), and 160 patients (17.6%) had improved, unchanged, and worsened grades, respectively. Preoperative functional status, gross total tumor removal, and histopathological type were significantly associated with mortality and functional outcomes. Conclusion Our findings demonstrate better postoperative functional outcomes in patients with fewer preoperative neurological deficits. Degree of resection, postoperative treatments, and prognoses are closely related to the histology of intramedullary tumors.