Bone remodeling is an essential physiological process in growth and healing. In modern systems deviations from normal bone physiology in the form of pathologies aid in the understanding of normal bone metabolism. Here we use external morphology and X-ray microtomography to diagnose and describe a metabolic bone disease in an amniote from the early Permian. The specimen consists of two fused tail vertebrae of a small varanopid from early Permian (289 million years old) cave deposits near Richards Spur, Oklahoma, USA. Inspection of the outer morphology reveals that the fusion encompasses the vertebral centra, zygopophyses and haemal arches, with the fusion zones distinctly swollen on the left side of the specimen. With visualization of its internal structure by microCT, this specimen is diagnosed as a complex metabolic bone disease. The radiological imaging suggests a pathologically high bone turnover rate, as shown by abnormal bone formation in some areas and increased bone resorption in others. This supports that the varanopid suffered from a metabolic bone disease similar to Paget's disease of bone as seen in humans today, which is linked to both genetic and viral factors. This finding extends the occurrence of Paget-like disease to the early Permian, and-provided a viral component was present-would also be by far the oldest evidence of viral infection in the fossil record.