We report the findings of a longitudinal observational study on HIV-infected patients grouped by presumed transmission group, who had diarrhoea. The purpose of this study was to assess the prevalence of and factors associated with Cryptosporidium infection on these patients. Modified formol-ether concentration followed by modified Ziehl-Neelsen and phenol-auraminc/carbol-fuchsin staining techniques were used to identify Cryptosporidium from 465 patients. Cryptosporidiosis was reported in 36/465 (8% and 95% confidence interval 6, 10) patients. Of the positive patients 30 (83%) were men and 6 (17%) women. Prevalence of infection was higher among HIV-seropositive patients whose exposure category was through sexual contact (69%) than among patients in other HIV exposure categories (9%, Standard Z test, P < 0.001). Median CD4+ cell count/mm3 was 120 (range 3-600). Besides diarrhoea, the main clinical manifestations were fever and weight loss in 14 (39%) and 26 (72%) patients, respectively. Cryptosporidium infection was considered to be the first AIDS defining disease in 31% of the patients followed by tuberculosis in 19%, Pneumocystis carinii pneumonia in 14%, Salmonella sepsis in 6%, isosporiasis in 3%, toxoplasmic encephalitis in 3%, leishmaniasis in 3% and Kaposi’s sarcoma in 3% of the patients. There was no significant difference (P = 0.82) in survival times for those given folate antagonists to treat other opportunistic infections. The decrease in prevalence of cryptosporidiosis observed from 1994 until May 1997 is not statistically significant (P = 0.11). Most cases of cryptosporidial infection in AIDS patients in Lisbon occurred in those whose HIV infection was assumed to have been acquired by the sexual route (hetero-, homo- and bisexual), with few cases occurring in drug-abusers.