A 54-year-old Japanese man presented to our university-affiliated hospital with a three-month history of lumbar pain. He was 167cm in height and weighed 58kg. An analgesic had been administered prior to his visit, but low back pain had persisted. His physical examination showed pressure pain and tapping tenderness at the third lumbar vertebral level, but no sensory or motor disorders of his lower extremities. His blood biochemistry showed no abnormalities and his medical history was non-contributory. A plain radiography revealed the formation of a vertebral spur or narrowing of the intervertebral disc between L3 and L4 as an age-related change, but no instability was evident between vertebrae and no obvious abnormalities were evident. Magnetic resonance imaging (MRI) of the L3 vertebral arch and spinous process revealed high intensity on T1- and T2-weighted imaging, and it was suppressed on fat-suppression imaging and no enhancement showed on gadolinium (Gd) contrast-enhanced imaging. Computed tomography (CT) imaging revealed an osteolytic change accompanied by marginal osteosclerosis in his third lumbar vertebral arch and spinous process, as well as a thinned and bulging bone cortex. Hounsfield units (HU) of CT for the area at which the osteolytic change was observed was −87HU, a value approximating that of fatty tissue, and areas of ossification or calcification were observed. Based on the above findings, although we suspected painful lipoma in the third lumbar vertebral arch and spinous process segment, we decided to perform a biopsy to confirm the diagnosis. Since a benign tumor was suspected, we planned to perform curettage of the tumor and to fill the defect with artificial bone. The operation was performed under general anesthesia. The third lumbar vertebral arch was exposed, and when an area approximately 1cm × 1cm in the external lamina of the right vertebral arch was opened, a yellow tumorous lesion with a color and elasticity macroscopically similar to those of ordinary fatty tissue was observed. The tumorous lesion was curetted away as much as possible, hydroxyapatite bone filler paste (BIOPEX®; HOYA Corporation, Tokyo, Japan) was used to fill the defect and the external lamina of the vertebral arch was replaced. Intraoperative pathological findings included hyperplasia of adipose cells and blood vessels, a small amount of trabecular bone and adipose cells of different sizes. Intraosseous lipoma was therefore diagnosed. His low back pain was improved immediately after surgery, and no recurrence of the tumor has been observed on CT imaging as of three years postoperatively.