Antibodies to Encephalitozoon cuniculi were examined by enzyme-linked immunosorbent assay using E. cuniculi PTP2 recombinant protein and by Western blot analysis on a total of 472 dog serum samples that had been collected in Japan. Of these samples, 21.8% (103/472) had antibodies against E. cuniculi. Each of 5 serum samples that showed high (>1.0) or low (<0.1) OD value was selected randomly and further examined by Western blot using E. cuniculi–native antigens. All samples with high OD values reacted with specific E. cuniculi proteins, including an antigen of approximately 35 kDa corresponding with PTP2; sera with low OD values did not recognize this E. cuniculi band. This study is the first to demonstrate the prevalence of E. cuniculi infection in dogs in Japan.