Objective To investigate the expression of HSPA9 and Beclin-1 in follicular thyroid carcinoma (FTC) and their roles in the occurrence and development of thyroid tumors. Methods Totally 57 cases of FTC tissue and corresponding adjacent tissues were selected, and the expression of HSPA9 and Beclin-1 protein were detected by immunohistochemistry method. The relationship between the expression of HSPA9, Beclin-1 and the clinicopathological features of the patients with FTC and the correlation between HSPA9 and Beclin-1 were analyzed. Results The expressions of HSPA9 and Beclin-1 in FTC were higher than those in normal tissues adjacent to cancer (P < 0.05); the positive rate of HSPA9 in patients with different pathological types and distant metastasis was significantly different (P < 0.05); the positive rate of Beclin-1 in patients with different pathological types was significantly different (P < 0.05). There was a positive correlation between the expression of HSPA9 and Beclin-1 in FTC (P < 0.05). Conclusions HSPA9 and Beclin-1protein may be closely related to the occurrence and development of FTC.