To determine the association of clinical characteristics with Cryptosporidium types and subtypes, faecal specimens from 2548 children with diarrhoea were screened by microscopy for Cryptosporidium spp., and positive specimens were genotyped and subtyped by PCR-RFLP. A total of 87 of the 2548 children (3.4 %) had cryptosporidial diarrhoea by microscopy and the majority (41.4 %) of the infected children were in the 4-8-year-old age group. Molecular characterization of the 83 children studied further (4 had mixed infections and were not subtyped) showed that Cryptosporidium parvum was the most commonly identified species (73.5 %) and consisted of three subtypes: IIa and IId were the most common (80.3 %), followed by IIc. Twentytwo (26.5 %) of the children had Cryptosporidium hominis and showed three subtypes: Id was the most common (54.5 %), followed by Ia (36.4 %) and Ie. Associated clinical manifestations varied between C. parvum and C. hominis. Diarrhoea associated with subtype Id, the most commonly identified C. hominis subtype, was more severe than that associated with other subtypes. In conclusion, this study confirmed a very different Cryptosporidium genotype and subtype distribution compared with other tropical countries among Kuwaiti children with diarrhoea, with a predominance of C. parvum IIa and IId. In addition, subtype Id of C. hominis was associated with more diverse and severe clinical manifestations in infected children, suggesting that parasite genetics may play an important role in the clinical manifestations of human cryptosporidiosis.