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Background Treatment of primary renal cell carcinoma using radiotherapy with curative intent is rare, because renal cell carcinoma is generally regarded as a radiation-resistant tumor. Recently, stereotactic body radiation therapy has been radically applied for cancers in various organs including renal cell carcinoma. However, there were few reports describing pathological changes of renal cell carcinoma post stereotactic body radiation therapy. This is the first report we are aware of documenting late histological effects of stereotactic body radiation therapy on renal cell carcinoma and surrounding normal tissue. Case presentation A right renal tumor was identified in a Japanese 70-year-old man on follow-up computed tomography for his chronic hepatitis. T1N0M0 renal cell carcinoma was clinically diagnosed as the tumor was 3 cm in diameter and well-enhanced with intravenously infused contrast material in the arterial phase on computed tomography. No metastases in regional lymph nodes or distant sites were evident. Stereotactic body radiation therapy was selected as an alternative therapy to surgery because of his poor liver function. A total dose of 60 Gy in 10 fractions over 12 days was delivered using a 10-megavolt X-ray. The renal tumor gradually decreased in size and partial response had been achieved at 2 years after completing stereotactic body radiation therapy. Hepatocellular carcinoma was identified during follow-up in the patient and he died of progression of hepatocellular carcinoma with hepatic failure 2.5 years after completing stereotactic body radiation therapy. Autopsy was done and it showed almost complete necrosis of tumor tissues with a small amount of viable renal carcinoma cells. These pathological findings suggested marked effects of stereotactic body radiation therapy on clear cell renal cell carcinoma. Conclusion Our case demonstrates a good pathological response with small foci of remnant viable cancer cells after stereotactic body radiation therapy of 60Gy in 10 fractions for small renal cell carcinoma. Although further experiences and longer follow-up are mandatory to conclude the optimal treatment schedule and efficacy of stereotactic body radiation therapy for renal cell carcinoma, stereotactic body radiation therapy may represent a novel less-invasive option for the treatment of primary renal cell carcinoma. [ABSTRACT FROM AUTHOR]