Background: The diagnosis of Giardia spp. may pose a challenge on routine Haematoxylin and Eosin (H&E) sections of small intestinal biopsy specimens. Additionally, clinicians may not order additional laboratory testing for Giardia at the time of the biopsy due to the frequently nonspecific clinical presentation. We selected cases diagnosed as positive for Giardia by H&E microscopy and tested the corresponding Formalin-Fixed, Paraffin-Embedded (FFPE) tissue using a quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to evaluate the performance characteristics in detecting Giardia. Design: We obtained 65 small intestinal biopsy specimens that were diagnosed as positive for Giardia on H&E sections from the years 1991–2012. We then tested the cases for evidence of Giardia by qRT-PCR using the FFPE tissue. Seventy negative control biopsies from the small intestine and colon were also tested. A single case diagnosed as equivocal for Giardia by H&E microscopy was also selected. A review of the medical records for the positive cases was done to determine whether any additional laboratory testing for Giardia spp. had been performed at the time of the biopsy. 

Results: Of the 65 biopsy specimens positive for Giardia by H&E, 64 also tested positive by qRT-PCR, resulting in a sensitivity of 98.5%. All 70 negative control cases were also negative by qRT-PCR, resulting in a specificity of 100%. The equivocal case tested negative for Giardia by qRT-PCR. Pertinent medical records were available for 21 of the Giardia-positive cases. Of these, only one case had a corresponding stool ovum and parasite examination, which was also positive for Giardia. The remaining 20 cases did not have any additional laboratory testing performed for Giardia at the time of the biopsy. Conclusion: qRT-PCR using FFPE tissue is a useful, highly sensitive and highly specific molecular adjunct to H&E histology in the diagnosis of Giardia, especially in equivocal cases. qRT PCR may help facilitate an accurate diagnosis in cases with nonspecific clinical presentations for which an endoscopic 
examination with biopsy is performed.