We have validated Giardia PCR positives using 9 different gene targets. Although each assay designed was capable of detecting virtually all the sequences for that target in the public databases, the number of Giardia samples detected using most of the assays was quite low suggesting a high degree of variability in the sequence of Giardia genes. The variability of Giardia species found in human samples was supported by mapping the Giardia assemblage. When using GDH as a PCR target some additional positives were observed that had a sequence that was most closely related to Giardia, but did not correspond to any sequence found in the databases. This suggests that a species closely related to Giardia exists that has not yet been sequenced. A similar situation occurred when validating Campylobacter positives using primers that were designed to detect all Campylobacter species. A wide diversity of Campylobacter species were detected in Australian clinical setting including some that were not present in any public database, but still most closely related to Campylobacter. We conclude that with the power of modern molecular diagnostics the complexity of infectious pathogens will increase.