The present study is the first to show overall prevalences of intestinal parasites among breeding kennel dogs in Japan. A total of 573 fresh fecal samples were collected from dogs at 12 breeding kennels. Giardia-specific coproantigen was examined by ELISA kit (SNAP(®) Giardia, IDEXX Laboratories, Inc., Maine, USA). Other intestinal parasites were determined microscopically using the formalin-ethyl acetate sedimentation technique. Overall prevalences of two genera of protists, Giardia spp. and Cystoisospora spp., were 25.7 and 1.2 %, respectively. The prevalence of helminthes was recorded as: Toxocara canis 0.2 %, Toxascaris leonina 0.9 %, Ancylostoma caninum 0.2 %, Trichuris vulpis 2.1 %, and Spirometra erinacei 0.4 %. According to age categories, Giardia spp., Cystoisospora spp., and T. leonina in <1-year-old dogs were significantly more prevalent than in ≥ 1-year-old dogs (61.0 vs. 19.8 %, P < 0.0001; 7.3 vs. 0.2 %, P < 0.0001; and 4.9 vs. 0.2 %, P < 0.001; respectively). With respect to fecal condition, the prevalences of T. leonina and T. vulpis were significantly higher in unformed stool dogs than in formed ones (2.4 vs. 0 %, P < 0.01, and 4.3 vs. 0.8 %, P < 0.05, respectively). In all of the breeding kennels except for one kennel, intestinal parasite infections were found at the high prevalent, ranging from 16.0 to 70.0 %.