CMV is a virus that is asymptomatic in healthy individuals but can cause serious mortality and morbidity in transplant patients and patients with acquired immunodeficiency syndrome (AIDS). Ganciclovir (GCV) is a nucleoside analog that significantly reduces morbidity and mortality in CMV-related infections and is used as the first choice in treatment. It is the first drug shown to be effective in the treatment of CMV disease in humans, and is also homologous to acyclovir. Long-term antiviral therapy is required to prevent or treat CMV disease, but this can cause antiviral resistance which was reported to be 8-14% in CMV. In CMV strains, GCV resistance is most common in the UL97 kinase gene region. The aim of this study was to investigate GCV resistance in CMV strains obtained from the patients with immune deficiency. A total of 49 patients, including 20 children, 29 adults, who were followed in the department of hematology were included in the study. Fifty-three samples from 49 patients with CMV DNA viral load >= 10(3) copies/ml were examined for GCV resistance. In the study, DNA sequences were determined by Sanger sequence analysis method 3500 Abi Prism Genetic Analyser (Applied Biosystems, Thermo Fisher Scientific, USA) in the 674 bp part of the UL97 gene region. The next generation sequencing (NGS) method was applied to the samples that could not be evaluated with this method. GCV resistance was not detected in 35 (66%) of 53 samples with the Sanger method. C592G, C607S and M4601 GCV resistance mutation was detected in three patients. Since the sequences were mixed, resistance analysis could not be evaluated with Sanger in 15 patient samples and the resistance was not detected in these samples studied with NGS. Antiviral resistance mutation was detected in three of 49 patients (6.1%). In 20 patients included in the study, three variant sequences (A442G, C592F, A427V) reported in the literature and determined to be sensitive to drugs by phenotypic tests and 78 variant sequences that were not reported in the literature were detected. As a result, the detection of antiviral resistance is important in the follow-up of the patients and guides the clinician in planning of the treatment. It was concluded that the samples that could not be evaluated with the Sanger method should be studied with NGS and further studies are needed to determine the role of the variant sequences detected for the first time in drug resistance.