Previous studies from African countries where HIV-1 infection is prevalent have shown that infections with Cryptosporidium parvum, Isospora belli and microsporidia are frequently associated with chronic diarrhoea in AIDS patients. The information about the occurrence of these parasites in HIV-2 associated AIDS cases with chronic diarrhoea is limited. We have performed a study of stool parasites in patients from Guinea-Bissau, the country with the highest prevalence of HIV-2 in the world. Stool specimens from 52 adult patients with chronic diarrhoea of which 37 were HIV-positive and fulfilling the clinical criteria of AIDS (five HIV-1, 28 HIV-2 and four dually infected with HIV-1 and HIV-2) were screened for parasitic infections. Twenty five percent of the HIV-2 positive patients were infected with C. parvum, 11% with I. belli and 11% with microsporidia, all three parasites were seen only in HIV-positive patients. The three patients with microsporidiosis, all HIV-2 infected, are to our knowledge the first cases reported from Guinea-Bissau. Other stool parasites such as Blastocystis hominis, hookworm and Strongyloides stercoralis were observed both among HIV-positive and HIV-negative patients.