Aim. Regardless a great progress in treatment, 15% of breast cancer cases remain lethal. One of the main problems in diagnosis and cure of this cancer type is its high clinical and genetic heterogeneity, and the identification of markers for personalized treatment is still a topical issue. Methods. Collection of clinical material, RNA isolation, and analysis of the ITSN2 and TKS5 isoforms expression using real-time quantitative PCR with fluorescence labeled probes. Results. The reliably reduced expression of ITSN2-S has been found in the HER2/neu-positive tumors with poor prognosis. There was no significant difference in the expression of ITSN2-L and TKS5-L in the analyzed samples. Conclusions. Our study has shown a potential use of the ITSN2 short isoform (ITSN2-S) as a breast cancer prognostic marker.