Fifty-two thoracic and 89 abdominal aspiration biopsy specimens assessed immediately by microscopic examination were evaluated prospectively. These biopsies were compared retrospectively with an equal number and type of biopsies that were not assessed immediately by microscopic examination. The comparison was made to determine whether the diagnostic accuracy and the complication rates of fine needle aspiration cytology would be improved by immediate microscopic assessment. The accuracy of fine needle aspiration biopsy with and without immediate cytologic assessment for the thoracic aspirates was 92% and 85%, and for the abdominal aspirates it was 74% and 81%, respectively. The complication rates with and without immediate assessment for the thoracic aspirates was 40% and 35%, and for the abdominal aspirates it was 7% and 6%, respectively. Immediate cytologic assessment did not change the accuracy or complication rates of fine needle aspiration biopsy significantly, but we believe that it provided greater educational benefits for fellows and staff in cytopathology and interventional radiology.