In an epidemiological investigation of trench fever in Japan, we compared the seroprevalence of Bartonella quintana in homeless people and in the general population. In homeless rescue outreach programs held in Tokyo from May 2001 to March 2003, 151 blood samples were taken from non-hospitalized homeless people. The prevalence of IgM and IgG antibodies against B. quintana in these people was compared with that in 200 healthy blood donors using a commercially available indirect fluorescent antibody test. Although IgG titers of > or = 1:128 were found in 57% (86/151) of homeless people and 51% (101/200) of blood donors, high titers of > or = to 1:1,024 were encountered only in homeless people (11%, 16/151). Attempts to isolate B. quintana from the blood of homeless people were unsuccessful, but polymerase chain reaction based detection, using Bartonella genus specific primers, demonstrated the presence of B. quintana DNA in the blood of 10 homeless people. Our data suggest that urban trench fever is endemic among the Japanese homeless population.