This study aimed to detect the frequency of Cryptosporidium infection and associated risk factors among children from rural areas in Peru. A case-control study was conducted, nested in a cohort in two rural communities that included children between 6 and 13 months who were followed for 6 months. Cases were children whose fecal samples tested positive for Cryptosporidium infection using an immunochromatography test. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) to analyze risk factors associated with Cryptosporidium infection. Among 72 children, 13 (18%) were cases. Cryptosporidium infection was associated with below secondary education of the mother (OR 7.62, 95% CI 1.50-36.72) and with having more siblings living at home (OR 1.71, 95% CI 1.04-2.82). An important frequency of Cryptosporidium infection among children from rural areas in Peru was reported, more research is needed to understand its true burden and risk factors among children in Peru.