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We studied the prevalence of intestinal parasites in animal companions in Saitama Prefecture, Japan, where no detailed data is currently available. Between May 1999 and December 2007, fecal samples were collected from 906 dogs and 1,079 cats in public animal shelters and examined by microscopy. Overall, prevalence of intestinal parasites in dogs was 38.6% and cats 43.1%. Trichuris vulpis was the most prevalent canine parasite species (22.3%), followed by Toxocara canis (12.5%), Ancylostoma caninum (10.4%), Isospora ohioensis (2.1%), Spirometra erinaceieuropaei (1.0%), Crypstosporidium sp. (0.9%), Giardia intestinalis (0.9%), I. canis (0.6%), Taeniidae (0.3%), Dipylidium caninum (0.2%), Echinostoma sp. (0.1%), and Pentatrichomonas hominis (0.1%). T. cati was the most prevalent feline parasite species (21.8%), followed by A. tubaeforme (13.2%), S. erinaceieuropaei (8.3%), I. felis (4.5%), Cryptosporidium sp. (2.8%), I. rivolta (2.2%), Pharyngostomum cordatum (1.6%), D. caninum (1.4%), Eimeria sp. (0.3%), Taeniidae (0.2%), Trichuris sp. (0.2%), Capillaria sp. (0.1%), Diphyllobothrium nihonkaiense (0.1%), and Metagonimus yokogawai (0.1%). Further molecular analysis to identify canine Taeniidae species and canine and feline Cryptosporidium species identified one canine taeniid positive species as Echinococcus multilocularis. Cryptosporidium species were identified as C. canis and C. felis. Parasites E. multilocularis and Cryptosporidium spp. in animal hosts were the first to be recorded in this prefecture. Compared to previous surveys conducted in the same area, the endemicity of some parasites appeared to have decreased, but some others remain. Given that most of these parasites have zoonotic potential, indicates the importance of having current data on parasite dissemination among animal companions. Government public health agencies should be responsible for educating pet owners about the control and prevention of zoonotic risk from such parasites.