Percutaneous fine-needle aspiration (PFNA) biopsy is an accepted technique for the diagnosis of suspected intrathoracic malignancy, but the appropriate indications for its use have not been clearly defined. To help establish guidelines, we performed a retrospective analysis of 188 patients who underwent PFNA biopsy for suspected intrathoracic malignancy. Biopsy led to a diagnosis in 72% (135/188) of the patients, but in 27% (50/188) samples were inadequate for cytological diagnosis, and in 2% (3/188) samples were adequate but failed to yield a diagnosis. Fifty-three patients underwent surgical intervention, thus allowing histological confirmation of the cytological diagnosis. In patients with a diagnosis from PFNA biopsy, operation confirmed malignancy in 97% (37/38) and a specific cell type in 79% (30/38). In patients without a diagnosis after biopsy, a malignancy was found in 73% (11/15) at the time of operation. This suggests a high rate of accuracy when PFNA biopsy provides a diagnosis. However, it also illustrates that a substantial percentage of PFNA biopsy attempts fail to yield a diagnosis in patients ultimately found to have malignancies. This implies that PFNA biopsy might best be reserved for patients who are not surgical candidates.