BackgroundMesenchymal stem cells (MSCs) derived from umbilical cord Wharton’s Jelly (WJ-MSCs) are emerging as promising therapeutics for a variety of diseases due to their ability of regeneration and immunomodulation and their non-tumorigenic and non-immunogenic properties. Although multiple protocols have been developed for WJ-MSCs isolation, insufficient cell numbers, heterogeneous cell population, and variations in procedures between different laboratories impede further clinical applications.MethodsWe compared six widely used WJ-MSCs isolation methods regarding cell morphology, yield, purity, proliferation rate, and differentiation potential. Based on these analyses, we developed a new isolation approach called “Mince-Soak-Digest (MSD)”, and compared its efficiency with the existing methods. Furthermore, we transplanted WJ-MSCs isolated by different methods to the rat uterus to test their ability for tissue repair.ResultsBased on the comparison and analysis of the six widely used isolation protocols, we identified that the inefficiency of the digestion of the extracellular matrix results in low cell yield. Thus, we have developed a robust and highly efficient method to isolate MSCs from WJ by incorporating a soaking step to facilitate the digestion of the extracellular matrix and release of the cells. Our newly developed method generates significantly higher cell yield (4 to 10-fold higher) than six widely used methods that we tested with high purity and consistency. Importantly, by transplantation of WJ-MSCs isolated by MSD to the rat uterus, we repair the endometrial injury and restore the fertility of the rats.ConclusionOur results provide a robust and highly efficient approach for isolating WJ-MSCs to restore injured tissue. The higher efficiency of MSD assures the abundance of WJ-MSCs for clinical applications. Furthermore, the reliability of MSD contributes to the standardization of WJ-MSCs isolation, which eliminates the discrepancies due to isolation procedures, thus facilitates the evaluation of the efficacy of WJ-MSCs across various human clinical applications.