Cryptosporidium parvum is usually considered to be the pathogen responsible for human cryptosporidiosis. We genotyped Cryptosporidium in 132 stool specimens from 80 Peruvian children, representing 85 infection episodes, using techniques that differentiate Cryptosporidium species and C. parvum genotypes. Five types of Cryptosporidium were identified: C. parvum human (67), bovine (8), and dog (2) genotypes, C. meleagridis (7), and C. fells (1). Twenty-five (29%) of the 85 infection episodes were associated with diarrhea. There was no significant difference in age, antecedent stunting, percentage with diarrhea, or duration of diarrhea for episodes with human genotype, compared with those of zoonotic Cryptosporidium. Duration of oocyst shedding was longer for human genotype than for zoonotic Cryptosporidium (mean, 13.9 days and 6.4 days, respectively; P = .004). Serum samples from 8 children with C. meleagridis, C. felis, or C. parvum dog genotype were tested for anti-human immunodeficiency virus (HIV) type 1 antibodies; all were found to be negative. Contrary to common belief, novel Cryptosporidium species and C. parvum genotypes can infect HIV-negative children.