Encephalitozoon cuniculi, a spore-forming obligate intracellular parasitic pathogen belonging to the phylum Microsporidia, has a unique and highly specialized organelle called the polar tube. Using an enzyme immunostaining assay in which germinated E. cuniculi spores were coated onto plastic surfaces, we tested healthy and human immunodeficiency virus (HIV)-infected individuals in Japan for anti-polar tube antibodies of each immunoglobulin (Ig) class. Anti-polar tube IgG was detected in just 4 of 380 healthy individuals; no anti-polar tube IgA was detected in any individuals; however, unexpectedly, anti-polar tube IgM antibodies were detected in 138 individuals (36%). When the healthy individuals were grouped by age, the highest rate of positivity to anti-polar tube IgM antibodies was seen in individuals aged 20 years old or younger. Fifty-nine percent (24/41) of the individuals aged 20 years or younger were anti-polar tube IgM antibody positive. This rate tended to decrease among individuals in older age groups. However, no anti-polar tube IgM antibodies were detected in 21 HIV-infected persons who were younger than 30 years of age and who had CD4 cell levels below 250/μl. These seroepidemiological results clearly indicate that circulating anti-polar tube IgM antibodies that are capable of strongly reacting with filaments extruded from geminated spores exist and suggest that such antibodies may play a part in protective immunity.