The distribution and public health significance of Cryptosporidium species/genotypes in pigs differ among geographic areas and studies. To characterize the prevalence of cryptosporidiosis in pigs in Henan, China, a total of 1,350 fecal samples from 14 farms in ten prefectures in Henan Province were examined. The overall prevalence of Cryptosporidium was 8.2% (111/1,350), with the highest infection rate (79/383 or 20.6%) in 1-2-month-old piglets and the lowest infection rates in 3-6-month-old pigs. Cryptosporidium-positive samples from 108 animals were analyzed by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of the small subunit rRNA gene, and 35 were further analyzed by DNA sequencing of the PCR products. Two Cryptosporidium species/genotype were identified, including Cryptosporidium suis (94/108) and the Cryptosporidium pig genotype II (14/108). C. suis infection was more common in younger piglets whereas the pig genotype II was relatively common in older pigs. These findings suggest that pigs are not a major source of zoonotic Cryptosporidium in the study area.