The systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are a diseases in which disturbances in plasma proteins glycosylation exist. The aim of the study was to compare the serum profile of transferrin isoforms between SLE and SSc. The study was carried out in 38 patients with SLE and 43 patients with SSc. Transferrin isoforms were analyzed by capillary electrophoresis method. Among the transferrin isoforms only the level of pentasialotransferrin in SLE patients was significantly higher than in SSc patients (p = .014). The median concentrations of trisialotransferrin and pentasialotransferrin were significantly lower in SLE patients (p < .001, p = .042; respectively) and SSc (p = .001, p < .001; respectively) than in the healthy subjects. In contrast, the level of tetrasialotransferrin manifested significant increase in comparison to the controls (p < .001 for all comparisons). The serum profile of transferrin isoforms alters in SLE and SSc but only level of pentasialotransferrin differs between SLE and SSc patients. We confirm that the serum profile of transferrin isoforms in SLE and SSc is unique to these diseases.