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.