Background: Patients presenting with a mass require tissue biopsy for histological diagnosis and treatment. Fine needle aspiration (FNA) is offered as an atraumatic, well tolerated, and inexpensive method for obtaining a biopsy from these lesions. Objectives: In this study we evaluated the accuracy of FNA as an atraumatic method among patients with nonthyroidal masses for diagnosis of neoplastic masses compared to open surgery. Patients and Methods: In a cross-sectional study, 65 patients with a head and neck masses (nonthyroidal) referred to us from 2004 to 2009. Those who had both FNA and open biopsy (the gold standard) were assessed for specificity, sensitivity, positive and negative predictive values of FNA in diagnoses. Results: Sixty-five cases with both definite diagnoses of open biopsy and FNA were assessed. The mean (± standard deviation) age of patients was 39.96 ± 19.69 years (range 10 to 82 years). Twenty-five (40.8%) subjects were categorized as malignant neoplasms, 16 (19.4%) as benign neoplasms, and 24 (39.8%) as non-neoplastic lesions. The sensitivity, specificity, positive and also negative predictive values of FNA in the diagnosis of neoplastic masses were 95%, 85%, 92.68%, and 91.66% respectively, and the diagnostic accuracy was 92.3%. Conclusions: It seems that FNA is a useful atraumatic diagnostic technique with a high diagnostic accuracy which can provide a highly sensitive diagnosis with low false positive diagnoses in patients with nonthyroidal masses.