Brown was diagnosed as HIV positive in 1988 and by 1993 was living with AIDS. Themes related to the HIV/AIDS pandemic appeared in Brown's work in the 1980s and continued throughout the rest of his career although he never wished to be a "one note artist" and continued to draw subject matter from almost every aspect of 20th century American culture. Despite experiencing painful side effects from medications and periods of hospitalization, the final years of Brown's life were some of his most productive. Between 1993 and 1997, Brown completed more than eighty paintings, and planned and executed home, studio, and garden designs. One of Brown's final large scale projects was a mosaic for the Howard Brown Health Center, a Chicago organization that provides healthcare to LGBTQ individuals.