In order to investigate the incidence of latent infections by parasites within the human digestive tract, we examined fresh stool samples from the colon of 31 patients (37-90 years, median age 71; 26 men and 5 women) collected within 12 hours of death. These subjects had been admitted to a university hospital in Yokohama, Japan, and died between April 2007 and December 2008 from causes other than parasitosis. Stool samples were fixed and stained for microscopic analysis, and PCR analysis for Entamoeba histolytica was performed for the parasite-positive samples. Results showed that ten out of 31 subjects were infected by E. histolytica only, one subject was infected by Giardia intestinalis only, and four subjects were infected by both E. histolytica and G. intestinalis. These findings are in contrast to conventional theories concerning general parasite infection in Japan, and indicate continuous or latent infection within the human digestive tract. The presence of pathogens such as E. histolytica and G. intestinalis in elderly or immuno-compromised patients is a serious issue and warrants further attention as a public health issue, particularly in relation to its mode of transmission.