Hematopoietic progenitor cell (HPC) transplantation is a treatment option for malignant and nonmalignant diseases. Umbilical cord blood (UCB) is an important HPC source, mainly for pediatric patients. It has been demonstrated that human leukocyte antigen (HLA) matching and cell dose are the most important features impacting clinical outcomes. However, UCB matching is performed using low resolution HLA typing and it has been demonstrated that the unnoticed mismatches negatively impact the transplant. Since we found differences in CD34⁺ viability after thawing of UCB units matched for two different patients (p = 0.05), we presumed a possible association between CD34⁺ cell viability and HLA. We performed a multivariate linear model (n = 67), comprising pre-cryopreservation variables and high resolution HLA genotypes separately. We found that pre-cryopreservation red blood cells (RBC), granulocytes, and viable CD34⁺ cell count significantly impacted CD34⁺ viability after thawing, along with HLA-B or -C (R² = 0.95, p = 0.01; R² = 0.56, p = 0.007, respectively). Although HLA-B*40:02 may have a negative impact on CD34⁺ cell viability, RBC depletion significantly improves it.