It is well known that Entamoeba histolytica, Giardia lamblia and Cryptosporidium spp can cause severe symptoms in humans. The diagnosis of these protozoan parasites depends on microscopic detection of their cysts or trophozoites in faeces. The aim of current study was to evaluate the use of three enzyme immunoassay (EIA) kits: Entamoeba CELISA (Cellabs diagnostic, Australia), Giardia CELISA (Cellabs diagnostic, Australia) and Crypto CELISA (Cellabs diagnostic, Australia) for detection of the above mentioned intestinal Protozoans. It also aimed to compare the performance of these immunoassay kits with microscopy called Ova and Parasite (O&P) examination tests namely, direct faecal wet smears preparations, formalin-ether concentration, Gomori's trichrome stain and auramine phenol staining routinely performed in the diagnostic Microbiology laboratory at Sultan Qaboos University Hospital. A total of 571 stool specimens were collected and examined by the three CELISA kits and the four microscopy tests. Giardia CELISA and Crypto CELISA were found to be more sensitive and specific than microscopy. The sensitivity of both kits was 100% and the specificity was 99% and 95% respectively. The performance of Entamoeba CELISA kit could not be established due to the small number of E. histolytica positive specimens. The enzyme immunoassay kits were easy to run and read compared to the cumbersome, labour intensive and more subjective O&P tests. The enzyme immunoassays may not replace O&P tests but may be used to confirm the clinical diagnosis of intestinal Protozoa.