Objective To investigate the expressions of aldehyde dehydrogenase 1 (ALDH1) and sex determining region Y-box protein 2 (SOX2) in breast cancer tissues and their clinical significance. Methods Immunohistochemistry was used to detect the expressions of ALDH1 and SOX2 protein in cancerous and its paracancer tissues of 80 patients with breast cancer treated in our hospital from 2017 to 2019, and to analyze the correlation between the expressions of ALDH1 and SOX2 protein, as well as the relationship between their expression and clinicopathological characteristics and prognosis of breast cancer patients. Results The positive expression rates of ALDH1 and SOX2 protein in breast cancer tissues were 75.0% and 62.5%, respectively. The positive expression rates of ALDH1 and SOX2 protein in paracancer tissues were 30.0% and 21.3%, respectively. The positive rates of ALDH1 and SOX2 protein expressions in breast cancer tissues were higher than those in paracancer tissues, and the difference was statistically significant (P<0.05). The expressions of ALDH1 and SOX2 proteins in breast cancer tissues were correlated with histological grade, TNM stage and axillary lymph node status of breast cancer (P<0.05). By Spearman correlation analysis, ALDH1 was positively correlated with SOX2 expression (rs=0.507, P<0.001). The univariate analysis of statistically significant indicators and the combination of clinical characteristics of the logistic regression multivariate analysis found that, breast cancer tumor size, histological grade, TNM stage, axillary lymph node status and ALDH1 protein and SOX2 protein expressions were not significantly correlated with those reaching disease-free survival (DFS) after follow-up (P>0.05, which may be affected by small sample size and small number of endpoint events). The Kaplan-Meier method was used to plot survival curves, and log-rank test results showed that the cumulative DFS rates of patients with positive ALDH1 and SOX2 protein expression were lower than those of with negative expression (P<0.05). Conclusions ALDH1 and SOX2 proteins are highly expressed in breast cancer tissues, and they are positively correlated. Survival curves show that positive ALDH1 and SOX2 proteins in breast cancer tissues tend to have a poorer prognosis.