Objective To investigate the immunohistochemical -characteristics of salivary gland adenoid cystic carcinoma (SACC), and the prognosis significance of CD117 expression in adenoid cystic carcinoma. Methods By the technology of tissue microarray and immunohistochemistry, expressions of Smooth Muscle Actin(SMA), p63 gene protein(p63), S-100 Protein, Cytokeratin-pan(CK-pan), Epithelial Membrane Antigen(EMA), Ki-67 Nuclear Antigen(Ki-67) and CD117/c-kit proto-oncogene(CD117) in 41 cases with SACC, 19 cases with salivary gland basal cell adenoma and 31 cases with salivary gland pleomorphic adenoma were observed. Expression intensities and distribution modes of the antibodies for the above proteins were summarized and analyzed for their significance in diagnosis, differential diagnosis and prognosis in SACC, basal cell adenoma and pleomorphic adenoma. Results Different distribution characteristics of SMA, p63, S-100 Protein, CK-pan and EMA were discovered among SACC, basal cell adenoma and pleomorphic adenoma. The marker of SMA, p63 and S-100 Protein was positive in the peripheral zones of tumor cells, the lining cells of sieve pores and the outer cells of gland tubular structures in SACC. It was also positive in the peripheral zones of tumor cells and outer cells of gland tubular structures in basal cell adenoma and positively diffused or nested in pleomorphic adenoma. The marker of CK-pan and EMA was strongly positive in thecytoplasm and cytomembrane of tumor cells in SACC positive in the cytoplasm of lining cells of the adenoid structures in basal cell adenoma and also positive in tumor cells differentiated from the epithelial cells and partially positive in tumor cells differentiated from the myoepithelial cells in pleomorphic adenoma. The marker of Ki-67, it was different between cases of SACC with different prognosis. There was a statistical difference between the recurrent survival cases or cases of death and no recurrent survival cases (the P value of SNK-q test was 7.4729 and 5.2186 respectively, P<0.01). A strong positive expression of CD117 was discovered in cases of death, and a statistical difference was found between them and the no recurrent survival cases (P=0.0394). There was a poor prognosis for cases with a high Ki-67 index and a strongly expressed CD117. Conclusion Different expressions of SMA, p63, S-100, CKpan and EMA may be valuable for the diagnosis and differential diagnosis of salivary adenoid cystic carcinoma, salivary basal cell adenoma and salivary pleomorphic adenoma. Expressions of Ki-67 and CD117 are related to the prognosis of salivary adenoid cystic carcinoma.