Limited data exist regarding the incidence of intestinal microsporidiosis following the introduction of highly active antiretroviral therapy (HAART) in Australia. At St Vincent's Hospital, Sydney, all faecal samples submitted for diarrhoea from HIV-infected patients between 1995 and 2006 underwent screening for microsporidiosis. A total of 3564 patients (7366 faecal specimens) was examined, resulting in 159 patients identified with microsporidiosis. The incidence of microsporidiosis declined from 11% in 1995 to 0% from 2004 onwards. At presentation the majority of patients were severely immunocompromised (median CD4 105 cells/mm(3)), with only 16% of patients on effective HAART. Twenty-four patients (24/76, 32%) died within a median of 22 months following microsporidiosis diagnosis. Significant predictors of AIDS-related mortality at presentation included the level of immunodeficiency and receiving no or ineffective HAART (P<0.05). Patients presenting after 1998 had a significant reduction in the risk of AIDS-related mortality compared with patients presenting before 1998 (hazard ratio 0.27, 95% CI 0.79-0.92). All 52 (68%) surviving patients were on effective HAART, with a median CD4 count 382 cells/mm(3) and HIV RNA of < 50 copies/ml at follow-up (median 4 years). The dramatic decline of intestinal microsporidiosis in our study reconfirms the importance of effective HAART in preventing advanced immunodeficiency, opportunistic infections and associated AIDS-related deaths.