Surveys of the prevalence of the intestinal protozoan Giardia spp. in animal populations have relied almost exclusively on the detection of cysts in fecal samples. We have determined the prevalence of Giardia spp. in beaver and muskrat populations in four northeastern states and Minnesota by using both the detection of trophozoites in mucosal scrapings from live-trapped animals at necropsy and the detection of cysts in fecal samples collected from kill-trapped animals. In muskrats the prevalence of Giardia infection was 36.6% by cyst detection in fecal samples (n = 790) from kill-trapped animals and 95.9% in live-trapped muskrats when the intestinal contents were analyzed for the presence of trophozoites (n = 219). Similarly, in beavers, Giardia infection was 9.2% by cyst detection in fecal samples (n = 662) from kill-trapped beavers and 13.7% in live-trapped animals examined for the presence of intestinal trophozoites (n = 302). The detection of trophozoites in mucosal scrapings from live-trapped animals consistently yielded a significantly higher prevalence for both muskrats and beavers than did the method based on detection of cysts in the fecal samples. The prevalence of Giardia infection in juvenile and adult live-trapped muskrats was similar (92.5 and 94.4%, respectively), but the prevalence in juvenile live-trapped beavers (23.2%) was significantly greater than that seen in the adult animals (12.6%). No difference in Giardia prevalence on the basis of sex was seen in either animal species. Regional variation, often statistically significant, was seen in the prevalence of Giardia in beavers in the northeastern states and Minnesota, but was not detected for muskrats.