Primary Ewing's sarcoma/primitive neuroectodermal tumor (ES/PNET) of the kidney is a distinct entity that can be mistaken for variety of round cell tumors. We report a rare case of ES/PNET of the kidney in a 35-year-old female patient diagnosed by fine needle aspiration cytology (FNAC) and confirmed by immunohistochemistry (IHC) and reverse-transcriptase polymerase chain reaction (RT-PCR). Ultrasound guided FNAC smears from the kidney mass showed a population of malignant small round cells with perivascular arrangement and focal rosette formation. IHC performed on the cell block, showed strong immunopositivity for CD99 (MIC2) and vimentin. Molecular analysis of the aspirate by RT-PCR confirmed the EWS-FLI type1 transcript. The application of RT-PCR on FNAC material for establishing a diagnosis of renal ES/PNET is being reported for the first time. FNAC also confirmed metastases in the right level I cervical lymph node. The utility of IHC and molecular techniques in diagnosis of such a rare case is stressed and relevant literature is discussed. Diagn. Cytopathol. 2012. © 2011 Wiley Periodicals, Inc.