Cryptosporidiosis was investigated on two alpaca (Lama pacos) holdings in the South-West of England. Diagnosis was initially confirmed in a cria with diarrhoea from each holding. Cohort faeces samples were subsequently collected and examined for presence of Cryptosporidium oocysts by immunofluorescence microscopy. On the first holding, 30 samples (24 adults, 6 crias) were tested, and oocysts were detected in three of the cria samples but in none of the adults. On the second holding, 14 floor faeces samples representing apparently healthy crias and one faeces sample from a cria with diarrhoea were collected. Oocysts were detected in four of the "healthy" faeces samples and the sample of diarrhoeic faeces. All isolates were confirmed as Cryptosporidium parvum using polymerase chain reaction restriction fragment length polymorphism of the cryptosporidium oocyst wall protein (COWP) and ssu rRNA genes. Sequence analysis of a 741bp region of ssu rDNA was carried out on nine of these and revealed high sequence homology with previously reported C. parvum isolates. This investigation highlights the possibility of alpaca crias subclinically shedding oocysts, which has implications for epidemiology and transmission in animals as well as raising zoonotic concerns for human contacts. Gene sequencing of UK isolates from South American camelids is also described for the first time.