To evaluate the clinical relationship between papillary thyroid microcarcinoma (PTMC) and Hashimoto's thyroiditis (HT). A total number of 168 patients with histologically confirmed PTMC were enrolled into this study and divided into two groups according to the presence (n=49) or absence (n=119) of concurrent HT. The clinicopathological characteristics between two groups were compared, including age, gender, tumor location, single or multiple lesions, tumor size, invasion of envelope, lymph node metastasis. The correlation between PTMC and HT was analyzed by multivariate logistics analysis. Furthermore, PTMC tissue removed during surgery were collected for immunohistochemistry to evaluate the expression of BRAF(V600E). Thirty-three percent (38/115) female patients with PTMC were accompanied with HT, which is higher than that of male patients (20.75%, 11/53). In PTMC patients with HT, the average age was younger [(42.18 +/- 9.84) vs. (46.35 +/- 11.23) years] and tumor size was smaller [(0.65 +/- 0.12) vs. (0.87 +/- 0.22) cm] compared with those without HT. Multivariate logistics analysis showed that concurrent HT was an independent risk factor for PTMC (OR 3.012, 95% CI 2.025 similar to 3.731, P<.05). The rate of positively stained anti-BRAF(V600E) was lower in the cases with HT than those without HT. The expression of BRAF(V600E) was weaker in female than male patients with HT. Additionally, the expression of BRAF(V600E) was relatively stronger in the patients without HT who suffered from invasion of envelope and lymph node metastasis. The risk of concurrent HT in PTMC patients increases predominantly. The concurrence of HT in PTMC is of higher incidence in female patients, younger age, smaller tumor size and lower incidence of envelope invasion and lymph node metastasis. Additionally, the expression of BRAF(V600E) is relatively weaker in PTMC patients with concurrent HT. For future work, large-scale perspective follow-up and epidemiological study may help to establish an effective PTMC risk-evaluation system for the patients with HT.