With various methods, BRAF mutations have been detected in 73.4% to 87.1% of papillary thyroid carcinomas (PTCs) in Korea. We assessed the ability of allele-specific polymerase chain reaction using a dual priming oligonucleotide system, compared with direct sequencing and pyrosequencing, to detect BRAF mutations in fine-needle aspiration specimens from 85 patients undergoing thyroidectomy. Final pathologic diagnoses were 55 malignant lesions and 30 benign lesions. We detected BRAF mutations in 47 (90%) of 52 PTCs by at least 1 method. The sensitivity of the dual priming oligonucleotide system (88.5%) was slightly higher than that of direct sequencing (82.7%) and pyrosequencing (86.5%). The specificity and positive predictive value of all 3 methods were 100%. The dual priming oligonucleotide system is a simple, rapid, and reliable method for detecting BRAF mutations. This method may be a useful adjunct tool to improve the preoperative diagnostic accuracy of PTC in fine-needle aspiration biopsy specimens.