<h3>Objectives</h3> We investigated the expression profile of tumor stem cell (TSC) biomarkers (CD44, ALDH1, OCT4, and SOX2) in salivary gland tumors (SGTs). The expression of these biomarkers was compared between pleomorphic adenomas (PAs), adenoid cystic carcinomas (ACCs), and mucoepidermoid carcinomas (MECs). <h3>Study Design</h3> Twenty cases each of PA, ACC, and MEC were selected. Immunoexpression of biomarkers was analyzed in parenchyma and stroma, based on the percentage of positive cells and staining intensity. <h3>Results</h3> Epithelial immunoexpression of ALDH1 was low in ACCs and higher in PAs compared to malignant SGTs (<i>P</i> < .001). Immunoexpression of OCT4 was related to tumors in minor salivary glands (<i>P</i> = .011) and myoepithelial differentiation (<i>P</i> = .009). MECs, but not PAs or ACCs, showed high immunoexpression of SOX2. This biomarker was related to the absence of myoepithelial differentiation (<i>P</i> < .001) and malignant behavior (<i>P</i> = .002). In most PAs, ACCs, and MECs, stromal immunopositivity was evidenced for the studied biomarkers, except for SOX2. Stromal immunopositivity for CD44, ALDH1, and OCT4 was significantly related to malignant behavior. <h3>Conclusions</h3> We suggest the presence of distinct subpopulations of TSCs in parenchyma and stroma of SGTs, which might play important roles in the pathogenesis of these neoplasms.