Cryptosporididal infection is one of the most common nonviral causes o
f diarrhoea in humans and livestock, worldwide. Most clinical infectio
ns cause acute transient diarrhoea but persistent infections may devel
op causing severe chronic, often life-threatening disease, particularl
y in immunocompromised individuals. The parasite is considered to be t
he most commonly detected enteropathogen affecting AIDS patients and p
resently no effective treatment is available. In the absence of effect
ive drugs to treat this ubiquitous infections, the control and clinica
l management of cryptosporidiosis depends upon rapid, accurate and sen
sitive identification and characterisation of the aetiological agent,
both in clinical specimens and environmental samples. Conventional det
ection of Cryptosporidium is time consuming, insensitive and generally
requires the skills of highly trained operators. Molecular biology ha
s provided the basis for the development of a new generation of diagno
stics. The detection and characterisation of isolates of Cryptosporidi
um using molecular tools are discussed.