Cryopreservation of cord blood nucleated cells for subsequent application in clinical practice is the only way of their long-term storage. The aim of this study was evaluation of the apoptosis stages and phosphatidylserine distribution in the nucleated cells membrane after cryopreservation by different methods. Nucleated cell fractions were frozen under the protection of the cryoprotectants with different mechanism of action. It was shown that nucleated cells isolation in polyglucin and subsequent freezing under 5% DMSO protection, as well as cells isolation by two-step centrifugation method and subsequent freezing under 10% of polyethyleneoxide (PEO) protection, allowed to keep intact most of the cord and peripheral blood cells. Cryopreservation of nucleated cells isolated using Ficoll, regardless of the used cryoprotectant, leads to significant disruption of the lipids asymmetric distribution in membrane and significantly reduces the number of living cells. It has been found that cord blood nucleated cells more resistant to damaging factors of cryopreservation than peripheral blood cells, that is shown in significant differences between the number of live cells in quite all cases before and after cryopreservation.