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Renal cell carcinoma  (RCC) with rhabdoid features is a rare subtype of RCC.  We describe the case of a 36-year-old man who presented with neck pain, and a head CT which showed two infiltrative masses in the vertebral bodies. An abdominal CT demonstrated a heterogeneous mildly enhancing mass in the superior pole of the right kidney with internal necrosis. A chest CT revealed multiple enlarged hilar lymph nodes. EBUS-guided FNA was performed. The smears and cell block material showed loose clusters and single neoplastic cells with large vesicular nuclei and prominent nucleoli and abundant eosinophilic cytoplasm with fine vacuoles and granules. The tumor cells were positive for CAM 5.2, P53, EMA (Focally positive), and negative for RCC and CD 10 by IHC and positive for the VHL W117fs mutation by Sanger sequencing. These results were consistent with the diagnosis of RCC with rhabdoid features, which is consistent with surgical diagnosis. To our knowledge, this is the first report of RCC with rhabdoid features diagnosed by endobronchial ultrasound-guided fine needle aspiration (EBUS-guided FNA).