Objective: To investigate the correlations of aldehyde dehydrogenase 1 (ALDH1) expression with the molecular subtypes and ATP-binding cassette subfamily G member 2 (ABCG2) of breast cancer. Methods: The specimens from 179 cases of breast cancer were divided into five molecular subtypes according to the immunological markers (ER, PR, HER2 and CK5/6), which were luminal A, luminal B, Her2-enriched, basal-like and breast-like subtype, respectively. The expressions of ALDH1 and ABCG2 of the specimens were detected with immunohistochemical staining, and the relationship between them as well as their relations with the clinicopathological factors of breast cancer was analyzed. Results: Of the 179 cases of breast cancer, ALDH1 positive expression was present in 43 cases (24.0%). The ALDH1 expression rate had significant difference among the different molecular subtypes of breast cancer (P=0.003). The positive expression rate of ALDH1 was 16.7% (17/102) in luminal A subtype, 21.4% (3/14) in luminal B subtype, 54.5% (13/22) in Her2-enriched subtype, 33.3% (8/24) in basal-like subtype and 17.6% (3/17) in breast-like subtype, respectively. The positive expression of ALDH1 had no significant relation with the ABCG2 expression (P=0.052). Both ALDH1 and ABCG2 expression were related to the administration of preoperative chemotherapy (P=0.027 and P=0.033) and ALDH1 expression was related to the HER2 expression (P=0.006). Conclusions: A small number of breast cancer cases have positive ALDHI expression and the ALDH1 expression rate varies among the molecular subtypes of breast cancer. The expression of ALDH1 has no obvious relation with ABCG2.