The present study aimed to investigate the value of liver fructose 1,6-bisphophatase (FBP1) and hypoxia-inducible factor-1α (HIF-1α) in the molecular subtyping of breast carcinoma. Tissue obtained from 60 surgical specimens from patients with breast carcinoma underwent immunohistochemical staining for cytokeratin 5/6, HIF-1α and FBP1. The variation in the expression levels of these markers and clinicopathological factors were compared between molecular subtypes. In addition, disease-free survival was compared between basal-like and luminal breast carcinoma, according to differing expression levels of HIF-1α and FBP1. The results revealed that HIF-1α expression was detectable in 20/60 (33.3%) of the breast carcinoma cases, and was positively associated with lymph node metastasis (P=0.007). HIF-1α-positive patients exhibited a shorter disease-free survival, compared with HIF-1α-negative patients with invasive breast cancer. The expression levels of FBP1 were positive in 33/60 tumor tissues (55%; P<0.001), and FBP1 expression was associated with nuclear grade (P=0.017) and tumor stage (P=0.012). In breast carcinoma, HIF-1α expression levels were significantly negatively correlated with FBP1 levels (r=−0.711; P<0.001). Cox regression analysis identified FBP1 and tumor size as independent prognostic factors. Therefore, the present study demonstrated that patients with basal-like breast carcinoma exhibited lower levels of FBP1 expression in tumor tissues, compared with patients with luminal type breast cancer, and that low or absent expression levels of FBP1 may be associated with reduced disease-free survival.