Overall, the HIV prevalence rate of Indonesia remains low at 0.16%, but the HIV epidemic in the country has been among the fastest growing in Asia. Indonesia now faces a concentrated epidemic mainly fuelled by injecting drug use and the sharing of contaminated equipment, unprotected paid sex and, to a lesser degree, unprotected sex between men.

HIV infection rates vary in Indonesian provinces. The two provinces of Papua (Papua and West Papua) face a generalized epidemic. In Papua province, the number of AIDS cases is 15 times higher than the national average and HIV prevalence is estimated at approximately 2.4%. Even higher infection rates have been recorded in remote highlands (3.2%) and less accessible lowland areas (2.9%). In West Papua, the number of AIDS cases is twice the national average.

Currently, an estimated 193,000 people live with HIV in Indonesia, up from 170,000 in 2005, and 110,000 at the end of 2003. It is estimated that 46% of people living with HIV are injecting drug users (IDUs) and 14% are clients of sex workers. AIDS-related deaths have also drastically increased from 2,300 at the end of 2003 to 5,500 in 2005.

In 2006, 2,873 AIDS cases were recorded, 82% of them men. Every year, an estimated 3,000 to 5,000 lose their lives to AIDS in the country, or 8-14 people per day.

As of December 2006, out of the estimated 20,577 people who had an advanced HIV infection, 5,100 of them (24.78%) were receiving ART. 50 In Papua, which presents a generalized epidemic, only 3% of people living with HIV had received ARV treatment.

The number of women infected by HIV has almost doubled from 15,000 in 2003 to 29,000 in 2005. As of December 2006, an estimated 2,563 pregnant women were HIV-positive in Indonesia. Women in stable relationships are increasingly becoming infected by their partners who are either injecting drugs or having multiple unprotected sexual relationships. HIV transmission between female sex workers and their partners is a cause of concern with 6.37% of female sex workers living with HIV in Jakarta (2003).

In 2006-2007, the percentage of most-at-risk populations tested for HIV and informed of the results doubled compared to 2004-2005.