Background and Objective: Specific differentiation processes to various cell lineages are closely associated with factors such as transcription factors, tumor suppressor elements and internal signaling pathways including vHL, Ecad, and Runx3. Epigenetics is an effective control mechanism of these factors, including several mechanisms such as methylation and acetylation. The main objective of this study was discovering the expression status of vHL, Runx3 and Ecad genes and determining the methylation patterns in the respective genes in hematopoietic cord blood stem cells. Materials and Methods: After isolating the stem cells from cord blood, expansion of the desired cells and DNA purification from the cells, in the first stage cDNA was constructed from the RNA, and PCR was performed for the genes under study. In later stages, the processed DNA from the previous stages was used for MSP reaction. Results: After PCR using designed primers to be used in Real-Time PCR and RNA derived cDNA of stem cells, it was found that all the genes under study were expressed in CD34+ stem cells. MSP in another stage of the study showed that Ecad and Runx3 genes are partially methylated and partially expressed, and vHL gene is not methylated and is completely expressed in this stage. Conclusion: There is substantial agreement between gene expression and epigenetic alterations, and study of all the three genes indicates their effective role in biology and function of these stem cells in Hematopoietic stem cells.