Perspectives on cell therapy using multipotent stem cells or progenitor stem cells are progressing rapidly. Therefore, biomedical research on cells detection method should in line with it. Flow cytometry technique is usually used quantitatively to see the presence of stem cells in different sources, such as blood, bone marrow, tissues, etc. Nevertheless, there is another modality that can be used as an alternative, i.e. polymerase chain reaction (PCR). This study aimed to know whether PCR could be used as an alternative method for replacing flow cytometry technique in detecting human mononuclear cells (hMNCs) derived from umbilical cord blood in the rat blood. Human mononuclear cells from umbilical cord blood were injected into rat tail's vein. Blood sampling was collected from the heart 30 minutes, 1 hour, 3 hours, 6 hours, 1 day and 7 days after injection. The blood was then analyzed with flow cytometry to determine the presence of hMNCs (CD34+ hMNCs) and PCR to determine the presence of human DNA (human chromosome 17 alpha satellite DNA; HSA17). Polymerase chain reaction could be detecting the presence of human DNA in all samples that are compared to the flow cytometry that also detect the presence of hMNCs in all samples. The results showed that flow cytometry and PCR technique have a similar trend pattern based on time dependent. Polymerase chain reaction techniques can be used as an alternative method in detecting the presence of hMNCs in the rat's blood equally to the flow cytometry.