Cryptosporidium spp. are organisms of public health importance and are known to infect numerous animal host. In the Philippines, information on Cryptosporidium is limited. In this study, stool samples from calves, goats, pigs, chickens and monkeys were collected and fragment of the Cryptosporidium heat-shock protein gene was amplified by polymerase chain reaction (PCR) to detect the infection. Pigs showed the highest rate of infection (34.29%) followed by calves (20.41%) and chickens (5.66%). This is the first record of Cryptosporidium infection in pigs and chickens in the Philippines. In addition, a fragment of the Cryptosporidium SSU rRNA [small subunit ribosomal RNA] gene was amplified and sequenced to genotype the isolates from the stool of calves. Cryptosporidium parvum and C. canis were identified. This is the first report of genotyping of Cryptosporidium spp. in the Philippines.