BackgroundRenal cell carcinoma is a potentially lethal cancer with aggressive behavior and it tends to metastasize. Renal cell carcinoma involves the inferior vena cava in approximately 15 % of cases and it rarely extends into the right atrium. A majority of renal cell carcinoma are detected as incidental findings on imaging studies obtained for unrelated reasons. At presentation, nearly 25 % of patients either have distant metastases or significant local-regional disease with no symptoms that can be attributed to renal cell carcinoma.Case presentationA 64-year-old Indian male with a past history of coronary artery bypass graft surgery, congestive heart failure, and diabetes mellitus complained of worsening shortness of breath for 2 weeks. Incidentally, a transthoracic echocardiography showed a “thumb-like” mass in his right atrium extending into his right ventricle through the tricuspid valve with each systole. Abdomen magnetic resonance imaging revealed a heterogenous lobulated mass in the upper and mid-pole of his right kidney with a tumor extending into his inferior vena cava and right atrium, consistent with our diagnosis of advanced renal cell carcinoma which was later confirmed by surgical excision and histology. Radical right nephrectomy, lymph nodes clearance, inferior vena cava cavatomy, and complete tumor thrombectomy were performed successfully. Perioperatively, he did not require cardiopulmonary bypass or deep hypothermic circulatory arrest. He had no recurrence during the follow-up period for more than 2 years after surgery.ConclusionsAdvanced extension of renal cell carcinoma can occur with no apparent symptoms and be detected incidentally. In rare circumstances, atypical presentation of renal cell carcinoma should be considered in a patient presenting with right atrial mass detected by echocardiography. Renal cell carcinoma with inferior vena cava and right atrium extension is a complex surgical challenge, but excellent results can be obtained with proper patient selection, meticulous surgical techniques, and close perioperative patient care.Electronic supplementary materialThe online version of this article (doi:10.1186/s13256-016-0888-5) contains supplementary material, which is available to authorized users.