PURPOSE: We aimed to evaluate a possible role for BRAF(V600E) mutation analysis of aspiration specimens in the work up of thyroid nodules classified as indeterminate on US. MATERIALS AND METHODS: A total of 122 nodules from 122 patients were prospectively classified as indeterminate nodules based on US findings. US-guided fine needle aspiration (FNA) was done for all 122 nodules. The presence of a BRAF(V600E) mutation in FNA specimens was determined by allele-specific PCR. RESULTS: US-indeterminate nodules were confirmed as malignant in 20.5% (25/122) of cases and benign in 76.2% (93/122) after FNA or surgery. A few (3.3% (4/122), remained indeterminate. A BRAF(V600E) mutation was identified in 14.8% (18/122) of USindeterminate nodules. Of those 18 nodules, three were benign and 13 were malignant after the initial FNA. One (0.8%, 1/122) with an initially benign cytology and a BRAF(V600E) mutation was confirmed to be malignant after surgery. The remaining two benign nodules with a mutation were not followed-up. All 9 initial FNA-nondiagnostic nodules were mutation negative but 2 (11.8%) of 17 indeterminate nodules on initial FNAs were mutation positive. CONCLUSION: BRAF(V600E) mutation analysis prevents false negative cytology for only 0.8% of cases and reduces ambiguous diagnoses for 1.6% of all US-indeterminate thyroid nodules. Therefore, adding BRAF(V600E) mutation analysis to FNA for US-indeterminate nodules is of limited usefulness.