Objective To investigate the expression of mitochondrial autophagy-associated protein PINK1 and Parkin in parotid pleomorphic adenoma (PA) and carcinoma ex pleomorphic adenoma(CA-EX-PA). Methods The expression of PINK1 and Parkin were detected by immunohistochemistry in 24 cases of normal parotid gland tissues, 32 cases of PA tissues and 42 cases of CA-EX-PA tissues. The correlations of PINK1 and Parkin expression with the clinicopathologic characteristics of CA-EX-PA patients were analyzed. Results The positive rates of PINK1 in normal parotid gland, PA and CA-EX-PA tissues were 100%, 91% and 67% respectively; and those of Parkin were 100%, 88% and 52% respectively. The expression rates of PINK1 and Parkin in PA and CA-EX-PA tissues were significantly lower than those in normal tissues (P < 0.05). The expression of PINK1 and Parkin protein were positively correlated in CA-EX-PA tissues (r=0.877, P < 0.01). In CA-EX-PA tissues, the expression of PINK1 and Parkin were associated with tumor invasion, lymph node metastasis and TNM stage (P < 0.05). Conclusion The expression of PINK1 and Parkin are decreased in PA and CA-EX-PA tissues. The decrease of mitochondrial autophagy activity might play important roles in the development, invasion and metastasis of parotid gland tumors.