Chronic lymphocytic leukemia (CLL) is considered an incurable disease due to the limited ability of current treatments to completely destroy leukemic cells. Repeated relapses may be caused by the expansion of rare resistant cells under the influence of the selection pressure of therapy. The aim of the study was to investigate the possibilities of identifying and characterizing rare populations of treatment-resistant CLL cells causing relapses and to monitor the presence of these cells during the course of the disease using single-cell RNA sequencing (scRNA-seq).