Diffuse pulmonary small nodules and pyrexia suddenly developed in a 27-year-old woman during immunosuppressive treatment for viral-associated hemophagocytic syndrome. Miliary tuberculosis was suspected, however, bone marrow biopsy did not support the diagnosis. Lung biopsy revealed interstitial pneumonitis admixed with characteristic inclusion-bearing cells, and cytomegalovirus (CMV) DNA was demonstrated in polymerase chain reaction using bronchoalveolar lavage cells, establishing the diagnosis of CMV pneumonitis. No other opportunistic pathogens were identified, and the pneumonitis was subsided due to administration of gancyclovir. The present case illustrates CMV pneumonitis as a differential diagnosis for small nodular opacities which develop in immunocompromised patients.