BACKGROUND: Fine-needle aspiration (FNA) cytology is increasingly being used as a diagnostic modality for soft tissue and bone lesions. These diagnoses can be challenging because of a variety of factors, including interpretation and sampling issues. This study investigates the diagnostic utility of FNA biopsy, in addition to the diagnostic pitfalls, in soft tissue and bone cytopathology. METHODS: We retrospectively reviewed the soft tissue and bone FNAs over a 4-year period (2004)(2005)(2006)(2007)(2008), along with available ancillary studies, pathological follow-up, and clinical data. The cases with a cytologic-histologic discrepancy were then reviewed. RESULTS: A total of 1114 soft tissue and bone FNAs were identified. Of the 1114 aspirates, 525 (47%) were positive for malignant cells, 505 (45.5%) were benign aspirates (including 189 benign lesions/neoplasms), 37 (3.5%) were inadequate, 34 (3%) had atypical cells, and 13 (1%) were suspicious for malignancy. Of the 586 cases (53%) with follow-up, including 445 cases with histological follow-up and 141 with ancillary studies, the overall sensitivity was 96%, the specificity was 98%, the positive predictive value was 99%, and the negative predictive value was 92%. A total of 15 false negatives and 3 false positives were identified with errors because of sampling (9 cases), interpretation (7 cases), and screening (2 cases). CONCLUSIONS: This large series demonstrates that there can be a high sensitivity and specificity in diagnosing bone and soft tissue lesions by FNA. Our data supports prior studies in the literature in showing that FNA cytology can be a valuable method for diagnosing these lesions. Cancer (Cancer Cytopathol) 2010;118:24-32.