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Background and importance Amputation neuromas consist of non-neoplastic collections of myelinated axons and Schwann cells and typically arise in injured peripheral nerves. Rarely, however, neuromas occur within the spinal cord. Intramedullary amputation neuromas have been described both with and without a history of trauma within the peripheral nervous system. We report a rare case of an isolated intramedullary spinal cord amputation neuroma. Clinical presentation This 43-year-old man presented with progressive and severe gait deterioration for ~ 7 years. Neurological exam revealed multiple positive findings consistent with cervical myelopathy, including positive Babinski and Hoffman signs, sustained clonus with patellar and Achilles reflexes, bilateral lower extremity weakness with increased muscular tone and spasticity, and inability to tandem walk. Magnetic resonance imaging demonstrated a 0.6-cm, homogeneously enhancing, intramedullary tumor with surrounding signal change at the C6 level. The lesion was excised and histologic examination revealed microscopic features compatible with an amputation neuroma. Conclusion Intramedullary amputation neuromas are rare and associated with either trauma or other CNS lesions. Our case represents an amputation neuroma in an unusual location in a patient without subjective preceding history of trauma or presence of a second lesion. .