Clinically significant cytomegalovirus (CMV) reactivation is not uncommon in patients with severe immunodeficiency secondary to underlying medical disorders or following aggressive immunosuppressive therapy. However, it is less frequently found in patients with low-grade haematological malignancies after nonintensive chemotherapy. We treated a patient at our centre for stage IVB follicular lymphoma with standard chemotherapy who successively developed CMV colitis associated with a CMV viral load of >3 million copies/ml. Four lines of antiviral treatment were necessary to obtain biochemical remission with undetectable CMV levels, with an initially insufficient response to valganciclovir despite therapeutic pre- and posttreatment levels. Subsequently, our patient also developed an infection with Pneumocystis jirovecii pneumonia (PJP) as further evidence of severe immune compromise. This case report demonstrates the importance of including investigations for less common sources of infection when confronted with a patient with a low-grade haematological malignancy and a pyrexia of unknown origin.