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Purpose To review our own experience with fine needle aspiration biopsy (FNAB) and frozen section (FS) in thyroid surgery and to assess the value of FNAB and FS in predicting malignancy in patient with thyroid disease. Methods The records of 300 patients who underwent thyroid surgery between April 2001 and June 2006 were analyzed. Results Of the 153 patients who had preoperative FNABs performed, 8 (5.22%) were reported as indeterminate, 100 (65.35%) were read as benign, and 3 (1.96%) were read as malignant. Fourty two of the FNABs were inadequate for evaluation (27.45%). When occult papillary carcinomas were excluded, sensitivity, and accuracy rates for FNAB reached 100%. One hundred and ninety one patients had FSs performed. 184 (96.33%) of these were reported as benign, 4 (2.09%) were reported as malignant, 3 (1.57%) were deferred to permanent paraffin (PP) sections. When occult papillary carcinomas were excluded, sensitivity, and accuracy rates for FS were 42.85%, 43%, and 97.28% respectively. Conclusions Our data supports the use of FNAB in the confirmation of malignancy and the need for operation. The routine use of FS is not warranted. Selective use of FS when FNAB is nondiagnostic or indeterminate may provide additional information. Both FNAB and FS fail to reveal occult carcinomas of thyroid. [ABSTRACT FROM AUTHOR]