In order to study the frequency of secondary infections of AIDS autopsy cases in Japan, especially the frequency of Mycobacterium aviumintracellulare complex (MAC) infection, retrospective autopsy study was conducted between 1986 and 1997 at the affiliated hospital of Institute of Medical Sciences, University of Tokyo. Secondary infections of various organs from 43 AIDS autopsy cases were examined using histopathology, genetic diagnosis of tuberculosis, Ziehl-Neelsen stain for acid-fast bacilli and immunohistochemistry. Nontuberculous mycobacterial infection (Mycobacterium avium) was observed in 17 cases (40%) out of 43 using polymerase chain reaction (PCR), but M. tuberculosis infection was not observed. Ziehl-Neelsen staining showed a positive reaction in lung and spleen tissues of 7 AIDS autopsy cases. Immunohistochemistry using anti-BCG antibody revealed positivity in 7 AIDS autopsy cases. CD4 counts of 17 AIDS patients with mycobacterial infection were less than 18.7/μl. Other opportunistic infections were also examined by histopathology. Secondary infections were present in every case, and these included cytomegalovirus infection (32 cases), Pneumocystis carinii (15 cases), Candida (16 cases), Aspergillus (12 cases), Cryptococcus (6 cases), Toxoplasma (6 cases), methicillin-resistant Staphylococcus aureus (3 cases), herpes virus (1 case) and Entamoeba histolytica (1 case). Malignant lymphoma was recognized in 14 cases and Kaposi's sarcoma in 6. This is the systemic report on secondary infections of AIDS autopsy cases in Japan. In diagnosis of mycobacterial infections, PCR was more useful than staining for acid-fast bacilli and immunohistochemistry. Secondary infections (especially mycobacterial infection) were closely associated with the low CD4 count.