Purpose: The risk of cytomegalovirus (CMV) reactivation following allogeneic hematopoietic stem cell transplantation (ASCT) reaches 30-50%, and there are numerous diagnostic tests to detect CMV replication. The most common tests used in this group of patients include 65kDa phosphoprotein (pp65) antigenemia immunofluorescence assay and nucleic-acid-based quantitative CMV-DNA polymerase chain reaction (qPCR). Material and Methods: In this study, patients who underwent ASCT and developed CMV positivity from 2009 to 2016 in our hospital were evaluated retrospectively. The study included samples of the same patient with antigenemia and CMV-DNA qPCR test for up to 48 hours. The study aimed to determine the factors affecting CMV DNA antigenemia and compare CMV DNA PCR and pp65 antigenemia immunofluorescence assay. Results: The results of 138 specimens of 39 patients who underwent ASCT were evaluated. The mean value of CMV PCR, which was positive for both tests, was 57.887 copies/ml (70- 1.213.633 copies/ml) and a significant correlation was found between the two tests and the positive samples (p = 0.018). The ROC analysis showed that 322 copies/ml CMV viral load in plasma corresponds to ≥1 antigen-positive cells/200 thousand leukocytes (Sensitivity: 68.5%; Specificity: 31.5%). CMV infection was observed in 32 samples; CMV DNA cut-off values of the reference according to CMV DNA PCR and antigenemia results, compared to the development of CMV infection, presented a significant correlation (p=0.004). Conclusion: Although there is a common agreement between antigenemia and CMV DNA PCR tests, one should keep in mind that the sensitivity of antigenemia test is low especially in the neutropenic period.