Background:
The actual burden of parasitic infections affecting Australians is relatively unknown. It is assumed that the estimated prevalence of protozoan infections is relatively similar regardless of the testing protocol employed. However scientific assessment of this has not been done; nor has a gold standard approach been determined for diagnosis of disease.

Methods:
A review of clinical specimen examined at four public Hospitals in Sydney, and the comparison of the outcome of different testing algorithms for the detection of enteric protozoa, for the period January 2007-December 2010.

Results:
The most frequently detected enteric protozoa were Blastocystis spp., identified in 5.4% (95%CI 5.0%-5.7%) of cases, Giardia intestinalis (1.1%; 95%CI 1.0%-1.2%) and Dientamoeba fragilis (0.8%; 95%CI 0.7%-1.0%). Detection of individual species using different testing algorithms differed between Hospitals (P<0.05). Permanent staining with iron haematoxylin staining (IHS) and modified IHS (mIHS) incorporating a carbol fuschin step method, consistently detected higher rates of Blastocystis spp, and G. intestinalis in comparison with light microscopy of wet preparations (P<0.001), and higher rates of G. intestinalis and Cryptosporidium when compared with screening enzyme immunoassays (EIA) (P<0.0002).

Conclusion:
Hospitals across Sydney employ different testing protocols for the detection of enteric protozoa. In this study, the modified IHS consistently detects more parasites than light microscopy of wet preparation and the EIAs. The development of a gold standard approach for diagnosis of enteric protozoa is therefore warranted Incorporation of molecular methods such as PCR would provide consistent and reliable estimates of the actual prevalence of enteric protozoa across laboratories.