Runt-related transcription factor-3 (RUNX3), being a tumor suppressor gene in gastric cancer, plays an important role in inhibiting cellular growth by participating in the transforming growth factor-beta-dependent apoptosis. The aim of this study was to determine the expression of RUNX3 in normal salivary glands and adenoid cystic carcinomas (ACCs), comparing the results with clinicopathological factors and patient survival. The quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis and Western blot analysis revealed the expression of RUNX3 both in normal salivary glands and ACCs. Nuclear and cytoplasmic immunoreactivities against RUNX3 in ductal luminal cells and acinous cells, but immunonegative in myoepithelial cells, were detected in normal salivary glands. In ACC, the RUNX3 immunostaining was shown in the cytoplasm of tumor cells; however, no nuclear location of RUNX3 was found. Lower RUNX3 expression showed significant correlation to distant metastasis and histological growth pattern (P = 0.009 and P = 0.025, respectively). On univariate analysis, low level of RUNX3 immunolabeling (P = 0.012), stage T4 (P = 0.017), lymph node involvement (P = 0.007), and distant metastasis (P < 0.001) were significantly associated with decreased overall survival. Multivariate analysis showed only distant metastasis had an independent prognostic effect on overall survival (P = 0.043). Our results demonstrate the expression of RUNX3 in normal salivary glands and salivary ACCs. The low level of RUNX3 protein in salivary ACCs might play a pivotal role in tumor progression and have prognostic values in ACCs.