We demonstrated that the diagnostic panel including the analysis of miRNA expression (miR-146b, -221, and -375), mRNA expression (HMGA2 and GCM2), the V600E mutation in the BRAF gene, and the ratio of mtDNA to nDNA enables accurate identification of parathyroid and thyroid tumors: PTC, MTC, HCC, and, with lower accuracy, malignant follicular tumors (PPV was 43.5% for the latter). Here, BRAF is linked to medullary thyroid gland carcinoma.