A cytomegalovirus (CMV) strain containing a mutation in the UL97 gene (Leu595Ser), which is known to confer ganciclovir resistance, emerged rapidly in a heart-transplant recipient after 54 days of antigenaemia-guided ganciclovir therapy. The emergence of this viral mutant, while the patient was receiving oral ganciclovir 1000 mg three times daily, was associated with increasing CMV pp65 antigenaemia levels despite the re-instatement of intravenous ganciclovir 5 mg/kg twice daily. The antiviral regimen was then switched to intravenous foscarnet 90 mg/kg, administered either twice daily, once daily or every other day, which resulted in a rapid decrease of CMV antigenaemia levels and prevented the development of CMV-associated disease. Frequent monitoring of the CMV viral load and/or mutational studies are warranted in highly immunocompromised transplant recipients to prevent the development of CMV disease caused by ganciclovir-resistant strains.