Objective To investigate the expression of immunoglobulin G4 (IgG4) and BRAFV600E genes in patients with thyroid nodules of uncertain significance and their role in the differential diagnosis of benign and malignant nodules. Methods 50 patients with thyroid nodule of uncertain significance were collected and the BRAFV600E gene mutation and serum IgG4 expression were measured. Using fine needle aspiration cytology as the gold standard, the participants were divided into benign group and malignant group. Pathological data, BRAFV600E gene mutation and serum IgG4 expression were compared between the two groups. The relationship between BRAFV600E gene mutation and serum IgG4 and malignant lesions of thyroid nodules was analyzed. Results Compared with benign group, the proportion of Bethesda class Ⅳ, BRAFV600E gene positive mutation rate and serum IgG4 level in malignant group were significantly increased (P＜0.05). Logistic regression analysis showed that Bethesda Class IV, BRAFV600E gene positive mutation and serum IgG4 level were all risk factors for malignant occurrence of thyroid nodules of uncertain significance (P＜0.05). The sensitivity and specificity of BRAFV600E gene in the diagnosis of benign and malignant nodules were 72.22% and 90.63%, respectively, which was consistent with the "gold standard" Kappa value of 0.644,and the sensitivity and specificity of serum IgG4 in the diagnosis of benign and malignant nodules were 81.97% and 75.00%, respectively, and the sensitivity and specificity of BRAFV600E gene and serum IgG4 in the diagnosis of nodule were 94.44% and 90.63%, and the Kappa value of the diagnosis consistent with the "gold standard" was 0.831. Conclusion The positive mutation rate of BRAFV600E gene and high expression of IgG4 in serum of patients with uncertain thyroid nodules are associated with higher risk of malignant nodules. The combined detection of BRAFV600E gene and IGG4 can improve the diagnostic efficiency of benign and malignant thyroid nodules with uncertain significance