The BRAF(V600E) mutation test has been more effective in thyroid nodules with suspicious US features than ones without suspicious features. Therefore, we investigated the role of the BRAF(V600E) mutation as an additional study to cytology in diagnosing a thyroid nodule without suspicious US features. This study was performed at Severance hospital from December 2010 through February 2012. During this period, 2,650 patients with 2,918 nodules underwent FNA with an additional BRAF(V600E) mutation test. Among them, we excluded thyroid nodules with suspicious US features. Finally, 485 thyroid nodules in 466 patients (mean age 50.3 years; range 9-80 years) were included in this study. We compared the differences between patients with malignant and benign thyroid nodules. We evaluated the detection rates of the BRAF(V600E) mutation according to the Bethesda System for Reporting Thyroid Cytopathology (BSRTC). There were 60 (60/485, 12.4 %) malignant and 425 (425/485, 87.6 %) benign nodules. The detection rate of the BRAF(V600E) mutation in thyroid nodules without suspicious US features was only 6.6 % (32/485). Most had malignant cytology (62.5 %, 20/32). For nodules without malignant cytology, only 12 nodules (2.6 %, 12/462) had the BRAF mutation. Among the 12 nodules, nine nodules were suspicious for malignancy on cytology. Additional BRAF mutation analysis shows additional diagnostic value in thyroid nodules with "suspicious for malignant" cytology alone even when the nodules do not show suspicious US features. Therefore, the test should be selectively performed in thyroid nodules without suspicious US features, considering cost-effectiveness as well as diagnostic accuracy.