BACKGROUND: Isosporiasis, a rare cause of diarrhoea among HIV-infected patients in the pre-highly active antiretroviral therapy (HAART) era, seems to be re-emerging. METHODS: A retrospective study was carried out for the period 1995-2003 in two hospitals in Paris to describe the prevalence, clinical characteristics and therapeutic outcome of isosporiasis in HIV-infected patients, and to compare the findings with those for cryptosporidiosis and microsporidiosis. RESULTS: The prevalence of isosporiasis increased from 0.4 per 1000 patients in the pre-HAART era (1995-1996) to 4.4 per 1000 patients in the HAART era (2001-2003), whereas the prevalence of cryptosporidiosis and microsporidiosis decreased. Compared with patients with either cryptosporidiosis (n=91) or microsporidiosis (n=58), patients with isosporiasis (n=28) more frequently originated from sub-Saharan Africa (72%), were more frequently female and heterosexual, and had a higher median CD4 count at diagnosis (142 cells/microL). All patients with isosporiasis presented with diarrhoea, which was severe enough to lead to hospital admission for 60% of them. Fever was uncommon (7%). All patients were treated for isosporiasis, 27 of them with cotrimoxazole. Relapse of isosporiasis occurred in six of 16 patients (38%) despite maintenance cotrimoxazole therapy and HAART. CONCLUSION: Isosporiasis in France occurs mostly in patients emigrating from sub-Saharan Africa and can induce severe diarrhoea. Relapse is common despite cotrimoxazole maintenance therapy.