Background: The HIV infection is associated with immunecompromised and rising in opportunistic infection. Therefore, it is predicted that death caused by HIV/AIDS would increase. The main problem for HIV/AIDS patients are opportunistic infection caused by Japanese Encephalitis (JEV) which is rarely found and diffi cult to diagnosed in Indonesia nowadays. Methods: This study is an observational descriptive. Cross sectional technique was used in this study. The amount of samples were 30 HIV/AIDS patients. Enzyme-linked Immunosorbent Assay (ELISA) was used to test IgG and IgM, and Real Time Polimerase chain reaction (RT-PCR). The sample was obtained from HIV/AIDS patients` blood, then CD4 and viral load were tested to detect JEV secondary infection. Results: There were 93,54% of HIV/AIDS patients have undergone ARV therapy for 1-3 years. HIV/AIDS is mostly sexually transmitted with 67,74%. The distribution of HIV/AIDS patients in stage I is 41,94%, 35,48% in stage II, and 22,58% in stage III. The HIV>4x102 viral load test revealed 20% of the samples are infected by JEV. The intention of MDGs (Millenium Development Goals) is to achieve no new infection, no discrimination, no death associated to AIDS are expected to contribute in order to decrease death through early detection of secondary infection. This study might be used as new policies in impeding HIV/AIDS, so the MDGs target could be reached. Conclusions: This research shows that ARV therapy is not enough to prevent secondary infection, such as JEV in HIV/AIDS patients. Therefore, it is necessary to give antimicrobes therapy and adequate nutrional supports.