Abstract: Objective To analyze the clinical application value of V-raf murine sarcoma viral oncogene homolog B1(BRAF)gene V600E(BRAF^V600E)mutation detection in the diagnosis of papillary thyroid cancer(PTC). Methods Totally 82 patients with PTC were selected as study group, and 80 patients with benign thyroid nodules were selected as control group. The mutation of BRAF^V600E gene in the preoperative biopsy tissue was detected by real-time fluorescence quantitative polymerase chain reaction(qRT-PCR)in both groups. The clinicopathological characteristics such as age, gender, status of papillary thyroid microcarcinoma(PTMC), number of lesions, extrathyroid infiltration, lymph node metastasis and TNM staging were analyzed in the study group. Results BRAF^V600E gene mutation was detected in 57 cases in the study group and 4 cases in the control group, the positive rates were 69.51% and 5.00% respectively, and there was significant difference between two groups(P<0.01). In the study group, the ratios of PTMC, N3 lymph node metastasis and TNM Ⅱ to Ⅳ in patients with positive mutation of BRAF^V600E gene were significantly higher than those in patients with negative mutation of BRAF^V600E gene(P<0.05). The area under curve(AUC)of BRAF^V600E mutation detection in the differential diagnosis of PTC and benign nodules, the diagnosis of PTMC and the clinical stage diagnosis of PTC were 0.823, 0.797 and 0.759 respectively, and the differences were statistically significant(P<0.05). Conclusion The positive rate of BRAF^V600E gene mutation is high in PTC tissue. The detection of BRAF^V600E gene mutation in lesion tissue by puncture biopsy before operation has - a certain application value in differential diagnosis, clinical stage diagnosis and pathological diagnosis of PTC, which can be used for auxiliary diagnosis and disease evaluation.