Objective: To investigate the BRAFT1799A gene mutation in papillary thyroid cancer (PTC) tissues and its relations with clinicopathologic features of PTC. Methods: Ninety-seven samples of PTC tissue along with 52 samples of normal thyroid tissue adjacent to PTC and 49 samples of nodular goiter tissue were collected. The BRAFT1799A gene mutations in these tissues were determined by nested PCR. The relations of BRAFT1799A gene mutation with clinicopathologic factors of PTC were analyzed. Results: In the 97 samples of PTC tissue, BRAFT1799A gene mutation was found in 49 samples (60.82%), while no BRAFT1799A gene mutation was found in samples of normal thyroid tissue adjacent to PTC and nodular goiter tissue, and the difference had statistical significance (P<0.05). In PTC patients, the BRAFT1799A gene mutation showed no significant relation with the gender, age and tumor size (all P>0.05), but was significantly related to the clinical stage, multiple foci, extra-capsular invasion, lymph node metastasis, thyroglobulin value after six months of standardized treatment and distant metastases (all P<0.05). Subtype classification of PTC showed that one case was eosinophilic cytoplasm variant PTC, one case was tall cell variant PTC, 46 cases were conventional PTC, and 49 cases were follicular variant PTC; there was no significant difference in mutation rates of the BRAFT1799A gene between conventional PTC and follicular variant PTC (63.04% vs. 61.22%, P>0.05). Conclusion: There is a high mutation rate of BRAFT1799A gene in PTC, and the BRAFT1799A gene mutation may probably have a close relation with the postoperative recurrence and metastasis of PTC.