Thyroid cancer is a rare disease that needs to be differentiated from the more frequent benign nodular goiter. The current, primary technique for distinguishing between benign and malignant nodules is by a fine-needle biopsy (FNB) cytological examination. This type of examination, unfortunately, often provides inconclusive results, and in recent years the introduction of molecular markers for the preoperative diagnosis of thyroid nodules has been proposed. This review covers current and emerging research in the diagnostic application of the BRAF mutation in papillary thyroid carcinomas. It considers the available literature related to the usefulness of preoperative BRAF mutation analysis as a diagnostic tool to refine inconclusive cytology. It also considers the available techniques used to detect this specific mutation. Many effective methods are now available to detect BRAF mutation in FNB material. Thanks to its high specificity, this genetic alteration is now considered a useful diagnostic marker for patients who have indeterminate thyroid nodule cytology and is a useful tool for thyroid nodule management despite its low sensitivity limiting its application. The authors believe that, in the future, the screening of genetic alterations will enter standard clinical practice as an adjunctive tool to conventional cytology, and larger studies will provide a better definition of the best, most cost-effective combinations of markers and methods.