We report the case of a 42-year-old woman who died in hospital from severe respiratory failure, 10 days after the onset of symptoms. Autopsy and microscopic examination identified features of diffuse alveolar damage in both lungs including hyaline membranes and intra-alveolar exudate. Gomori's methenamine silver stain of pink frothy materials in these exudates revealed thin-walled and cup-shaped microorganisms and a diagnosis of Pneumocystis jirovecii pneumonia was made. There were small granulomas in the pulmonary interstitium and hepatic lobules representing an unusual inflammatory reaction against Pneumocystis jirovecii. Extrapulmonary involvement with pneumocystis infection is a rare event occurring in 1% to 2% of all pneumocystis cases. Screening and confirmatory tests for human immunodeficiency virus (HIV) detection were positive. There was no information available regarding the patient's medical history or the possibility of HIV infection prior to the autopsy, because the patient was a foreign worker who arrived in Korea 2 months before her death. Medical examiners often perform autopsies with limited information regarding the deceased person, even when person is a Korean national. Therefore, an awareness of protection protocols during autopsy, as well as of the atypical patterns of critical diseases, is crucial.