Thyroid carcinoma is the most common endocrine malignancy, and papillary thyroid carcinoma (PTC) comprises almost 80% of all thyroid cancers. The incidence of PTC is increasing, and it may pose both diagnostic and clinical dilemmas, especially in those cases where morphology alone is insufficient to provide a definitive answer. Recent progress in the discovery of molecular alterations in PTC, and availability of molecular techniques enabling their detection in surgical and cytologic samples have resulted in an explosion in the literature, documenting the utility of molecular testing for diagnosis and prognostication of patients with suspected PTC. Out of several genetic mutations known to occur in PTC, BRAF V600E mutation is the most common and appears to be the most helpful in improving the accuracy of cytomorphological analysis of thyroid fine-needle aspiration samples, particularly of samples with indeterminate cytology. Furthermore, BRAF mutation also helps in the prognostication of these tumors, serving as a marker of more aggressive PTC. Herein, we provide an illustration of diagnostic usefulness of BRAF mutation detection in thyroid fine-needle aspiration samples, and discuss the diagnostic and prognostic role of this mutation.