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Abstract Backgrounds Although calcifications have been observed in various renal masses, osseous metaplasia has very rarely been reported. Here, we present a case of concomitant clear cell renal cell carcinoma with osseous metaplasia and papillary thyroid microcarcinoma. Case presentation A 52-year-old male was being investigated for having post-prandial gaseous abdominal distention. Computed tomography of the abdomen showed a heterogeneous mass lesion measuring 27 × 24 mm at the upper/mid pole of the right kidney. It also revealed two small (10 and 11 mm) benign bone islands in the body of the D4 and L4 vertebrae. The patient underwent a metastatic workup by computed tomography, which revealed a 93 × 35 mm mass in the left thyroid lobe with coarse calcification. A partial nephrectomy was planned for the renal mass, but the site of the mass deemed this impossible. Six months after the operation, the patient underwent total thyroidectomy. Histopathology of both tissue samples revealed concomitant clear cell renal cell carcinoma with heterotopic bone formation and papillary thyroid microcarcinoma. Conclusion Although rare, osseous metaplasia in renal cell carcinoma can occur and may indicate an early-stage carcinoma with a favorable prognosis.