The examination of archival pathology specimens of human small intestine by light microscopy, field emission scanning electron microscopy (FESEM), and confocal scanning laser microscopy using fluorescent in situ hybridization (FISH) techniques was undertaken to better understand the epidemiology of Giardia. Giardia trophozoites were tentatively identified in the light microscope after hematoxylin and eosin (H&E) staining. The organisms were adherent to the intestinal epithelium where they were also associated with strands of mucus within the lumen. Fluorochrome-conjugated antisense oligonucleotide probes, developed for the 16S rRNA of Giardia lamblia and Giardia muris, were used in FISH experiments with confocal scanning laser microscopy. Positive identification of trophozoites could be obtained with the G. lamblia probe, but not with the G. muris probe. FESEM examination of serial sections adjacent to FISH-stained sections revealed trophozoites characterized by their morphological features. The 16S rDNA probes specifically distinguished different species of Giardia, but whether multiple infections can occur within an individual host could not be determined.