BACKGROUND: Regular monitoring of cytomegalovirus (CMV) reactivation in children who undergo transplantation is performed by molecular testing on blood samples. This highlights the need to explore noninvasive alternatives, such as saliva. The present study evaluated the usefulness of saliva samples for detecting and monitoring CMV reactivation in children undergoing transplantation at a referral center in Lima, Peru. METHODS: A total of 85 paired samples of liquid saliva and whole blood and 91 paired samples of swab-collected saliva and whole blood from 16 children who underwent transplantation were analyzed by quantitative polymerase chain reaction (qPCR). RESULTS: The positivity rates for whole blood, liquid, and swab-collected saliva were 12.59%, 15.29%, and 12.09%, respectively. No significant differences were observed in viral load among the samples, and there was no remarkable correlation or agreement between saliva and whole blood. However, 19 samples from 4 patients were positive in their saliva but negative in their respective whole blood pairs. One patient who was positive in both the saliva samples and negative in blood developed gastrointestinal CMV disease. CONCLUSIONS: Saliva may serve as a promising diagnostic tool for detecting and monitoring CMV reactivation in pediatric transplant recipients. Further studies should explore the significance of the saliva viral load to guide pre-emptive therapy and predict disease development.