Background: The BRAF(V600E) mutation is common in papillary thyroid cancer (PTC). Lymph node metastasis (LNM) may be associated with poor prognosis. However, the LNM mechanism remains unclear. Objectives: Our aim was to evaluate the prevalence of the BRAF(V600E) mutation in primary tumors and accompanying LNM at the time of diagnosis. Methods: This retrospective study included 51 PTC patients (40 women, 11 men; mean age 40.0 +/- 16.5 years; range 6-81) who underwent total thyroidectomy accompanied by a lateral neck dissection due to preoperatively detected LNM. Real-time PCR was used for the detection of the BRAF(V600E) mutation in specimens from primary thyroid tumors and metastatic lymph node tumors. Results: The prevalence of the BRAF(V600E) mutation was 64.7% (n = 33) in primary tumors and 47.1% (n = 24) in metastatic lymph nodes. Of 33 patients with BRAF(V600E)-positive primary tumors, 18 (54.5%) had BRAF(V600E)-positive metastatic lymph nodes. Of 18 patients with BRAF(V600E)-negative primary tumors, 6 (33.3%) had BRAF(V600E)-positive metastatic lymph nodes. The presence of the BRAF(V600E) mutation in the primary tumor did not affect the tumor size, but the diameter of metastatic lymph nodes significantly increased (by nearly 3 mm) with the presence of BRAF(V600E) in LNM (p = 0.01). Conclusions: In our study, the BRAF(V600E) mutation did not show a one-to-one correspondence. This indicates that the presence of BRAF(V600E) in the primary tumor is not clonal and addresses the role of intra-tumor heterogeneity in PTC tumorigenesis. This supports the theses that mutations occur in the later stages of tumorigenesis, might be subclonal, and develop de novo, or that some other factors may be involved in the development of metastasis.