To determine the prevalence of Giardia genotypes in post-weaned dairy calves, fecal specimens were collected from 3 to 11-month-old dairy calves per farm on two farms in Vermont, New York, Pennsylvania, Maryland, Virginia, North Carolina, and Florida. Specimens cleaned of fecal debris and concentrated using CsCl density gradient centrifugation were stained and examined by immunofluorescence microscopy and also subjected to PCR and DNA sequence analysis. Overall, PCR provided more sensitive detection than IFA. Prevalence of Giardia infection, as detected by PCR ranged from 20% on NC-2 to 81% on VT-2, with an overall prevalence of 52% (237 positive samples out of 456 total). DNA sequence analysis of the 16S rRNA gene revealed 87% of the 237 Giardia isolates were Assemblage E, and 13% were Assemblage A although the prevalence of these genotypes varied greatly from farm to farm, with five farms having no Assemblage A Giardia. Therefore, Assemblage E was present in 45% of all animals tested and Assemblage A was present in 7% of the animals. Thus, while many of the calves were infected with a genotype that is not known to be infectious for humans, post-weaned calves on nine of 14 farms did harbor Assemblage A Giardia. Therefore calves should be considered as a potential source of human infectious cysts in the environment, with some farms representing a much higher risk than others.