Introduction: Cryptosporidium spp. (C. spp.) cause morbi-mortality in children with AIDS. Objective: To identify the association between viral load, CD4 levels and C. spp., presence in feces of children with AIDS. Methods: Observacional study in children of the Hospital Universitario del Valle of Cali. Data like age, gender, origin, consanguinity, treatment, stage, maternal survival and weight, were taken. Feces were analyzed by the technique of Ziehl-Neelsen modified. Viral load and CD4 levels were measured. Statistic included stratified analysis, models of logistic regression, and tests, Student t, χ2, and Fisher exact, being significant P < 0.05. Results: Were analyzed 72 children between 0 and 15 years, 52.7% masculine ones, 50% consanguinity and with alive mother, 54.2% of the urban area, 69.1% institutionalized ones, 36.1% severity degree C, 73.6% with analog nucleoside with protease inhibitor, 55% with >100,000 copies of viral load and >100,000 cells CD4. The prevalence of C. spp. was 51.4%, being more affected between 5 to 10 years; with a greater proportion of positive children for C. spp. with severe degree for AIDS (P = 0.03). With interval of confidence of 95%, >2 years had a greater risk 8 times to be positive in feces for C spp. (1.6-40.1); for age, gender and rural origin, 7.7 (1.5-38.9); alive mother and to be institutionalized, 6.1 (1.1-32.7), and for severity of the disease and weight, 5.7 (1-32.3). Conclusions: The prevalence for C. spp. was 51.4%, with risk factors age >2 years and degree of severity C, without significant differences in weight, viral load and CD4 levels.