Protozoa are important enteric pathogens in patients with human immunodeficiency virus (HIV) infection. In this study the prevalence of intestinal protozoa in 154 HIV-infected patients, with or without diarrhoea, in our region (Apulia, South Italy) was evaluated between December 1993 and February 1998. In the majority of patients CD4+ T cell count was below 200/μl. The overall prevalence of intestinal protozoa was 43/154 (27·92%). Twenty-eight (43·08%) out of 65 patients with diarrhoea and 15 (16·85%) out of 89 non-diarrhoeic patients were parasitized. In particular, in the group of 65 patients with diarrhoea the following protozoa were identified: Cryptosporidium parvum in 14 (21·54%), Blastocystis hominis in 7 (10·77%), microsporidia in 6 (9·23%), Giardia lamblia in 4 (6·15%) and Isospora belli in 1 (1·54%). Three patients were Cryptosporidium parvum-microsporidia co-infected. In patients without intestinal symptoms, prevalence was 3/89 (3·37%) for Cryptosporidium parvum, 9/89 (10·11%) for Blastocystis hominis, 1/89 (1·12%) for microsporidia and 2/89 (2·25%) for Giardia lamblia. A significant (P<0·001) correlation was observed between protozoan infection and the presence of diarrhoea. In particular, Cryptosporidium parvum and microsporidia infections were significantly (P<0·001) and P=0·046, respectively) associated with diarrhoeal illness. Moreover, the majority of cases of cryptosporidiosis were first diagnosed in the periods of heaviest rainfall. Therefore, drinking water contamination may be a possible source of human infection in our area.