Isospora belli, Cyclospora cayetanensis as well as several species of microsporidia are recognized as emerging protozoan
pathogens of humans. All are obligate intracellular parasites, with Isospora and the microsporidia being primarily
associated with immunocompromised hosts. Cyclospora is a cause of traveller's diarrhoea, and is responsible for water-borne and food-borne outbreaks of disease. Drug treatment is available for these infections. Improved diagnostic methods
including the autofluorescence of I. belli and C. cayetanensis oocysts have assisted in the routine detection of these
pathogens. Since the recognition of immunosuppression due to HIV infection, microsporidia have become recognized as
important human pathogens with a continuing expansion of the parasite-associated clinico-pathological spectrum. The
small size, intracellular nature and poor staining properties with many histological stains result in under-reporting of
microsporidial infections. Trichrome stain and optical brighteners are used to detect spores in faeces, urines, respiratory
secretions and other aspirates. Electron microscopy remains an important diagnostic method but its sensitivity is relatively
poor. Molecular techniques should overcome current diagnostic limitations. The ability to extract DNA and amplify by
PCR directly from clinical samples has increased the usefulness of molecular methods. Restriction fragment length
polymorphism analysis of amplicons can be used to determine genus, species and strain types of various microsporidia.
Increased specificity is required in primer design because current primers used for amplifying non-microsporidian DNA
also amplify microsporidian DNA. Diagnosis and pathogen characterisation rely increasingly on PCR-based approaches,
and the sequence analysis approach becomes increasingly feasible and affordable. However, robust, reliable and sensitive
methods are still required for dissecting pathogenesis, epidemiology, transmission routes and sources of infections.