We surveyed the rates of internal infection of swine with gastrointestinal tract protozoa by checking the stools of 334 pigs (suckling pigs, growing pigs aged 1 to 6 months and sows or sow candidates) on 8 hog farms in Saitama, Japan from September to November 2009. Oocysts and cysts per gram of stools in all pigs were calculated. Parasite detection rates were statistically analyzed for each of the farms, age groups, and stool condition scores, and the relationship between parasitic infection and diarrhea was investigated. Cryptosporidium was detected in 79 pigs (23.7%) of all pigs checked, Giardia was found in 53 (15.9%), Balantidium in 155 (46.4%), and coccidium in 20 (6.0%). The rate of Cryptosporidium infection was higher in the 2- and 3-month-old groups (55.6 to 60.0%) than in the others (2.5 to 27.6%) (P < 0.05): oocysts per gram of stools of 10⁴ to 10⁵ were detected in a total of 33 suckling pigs and 2- and 3-month-old pigs, including 10 of an outdoor farm. There was a correlation between the infection rate and diarrhea in five piglets aged 1 month or younger. In addition, the number of 6-month-old pigs infected with Giardia was 40.0%, as opposed to just 5.1% (P < 0.05) of suckling pigs. Detection rates differed among farms. The Balantidium infection rate was high in pigs older than 4 months (45.0 to 78.9%), as opposed to 15.4 to 17.2% (P < 0.05) in pigs younger than 1 month.