This case report highlights a diagnostic pitfall involving a pediatric patient with suspected cytomegalovirus (CMV) infection, where initial CMV PCR results were false-negative due to viral sequence variation. The patient's clinical presentation and specific symptoms are not detailed in the provided snippet, but the core issue revolves around the unreliability of PCR when viral genetic mutations occur. Subsequent investigation revealed the variant, emphasizing the importance of considering viral genomic diversity in diagnostic testing. Accurate CMV diagnosis is crucial for immunocompromised patients to prevent serious consequences. Teaching point: Viral sequence variations can lead to false-negative PCR results, necessitating careful interpretation and potentially alternative diagnostic methods.