A cross-sectional study was done between October 2014 and June 2015 to estimate the frequency of infection due to intestinal coccidiosis in children admitted to a hospital in Peru, and compare the modified acid-fast staining procedure with the enzyme-linked immunoassay (ELISA) method for the detection of Cryptosporidium spp. Coccidia were detected using the modified acid-fast staining procedure and the Cryptosporidium ELISA method (kit r-Biopharm) on seriated stool samples. Out of a total of 325 children, 5.5% had some type of intestinal coccidiosis: 3.7% involved Cryptosporidium spp. (using both techniques) and 1.8% involved Cyclospora cayetanensis (using the modified acid-fast staining procedure). The modified acid-fast staining procedure and ELISA method revealed a 0.955 consistency in the detection of Cryptosporidium spp. In conclusion, intestinal coccidiosis is frequent in children based on the population studied; similarly, both techniques can be used to detect Cryptosporidium spp., but the modified acid-fast staining procedure has an advantage over the other because it is cost-effective and can detect other coccidia in everyday practice.