Breast carcinoma is one of the most common neoplasia and the first cause of women cancer related deaths worldwide. In the past few years with diagnostic increment, the number of patients diagnosed with ductal carcinoma in situ (DCIS) increased considerably and opened up new ways in research and new dilemmas in diagnostic and clinical practice. This work aimed to evaluate differences in Galectin-1 and Galectin-3 expression and lectins ligands profile on DCIS cells in hypoxic microenvironment. Lectin histochemistry and immunohistochemistry were performed with Concanavalin A, Wheat Germ Agglutinin, Peanut Agglutinin and Ulex europaeus Agglutinin lectins and with anti-Galectin-1 and anti-Galectin-3 antibodies. Lectin ligands were more recognized in hypoxic lesions by Concanavalin A (p = 0.0019), Wheat Germ Agglutinin (p < 0.001) and Ulex europaeus Agglutinin (p = 0.0014), but not by Peanut Agglutinin (p = 0.5779) when compared to non-hypoxic. Galectin-1 was not observed in all cases analyzed on both groups, differing from Galectin-3 that was overexpressed on cytoplasm of DCIS hypoxic group in relation to control group (p = 0.031). As far as we are concerned, this is the first paper that describes glycobiological alterations in breast cancer hypoxic environment in vivo that could be used to validate in vitro models on this aspect. Moreover, comedogenic/necrotic carcinomas were usually associated with poor-prognostic than others, and our results show that glycosylation may play an important role in this event.