The nested polymerase chain reaction (PCR) was used for direct species-specific detection of Coxiella burnetii in blood samples from 52 patients with chronic nonspecific symptoms, but no diagnostic or treatment history of Q fever. All patients had been in ill-health with general fatigue, muscle and joint pain, headache, etc., for one to more than 10 years. Seventeen (33%) showed evidence of C. burnetii infection, based on amplification of 438-bp fragments specific to C. burnetii by nested PCR, and 94% of positive patients reported close contact with animals. In contrast, five (9.6%) of 52 samples from healthy adult controls and two (2.8%) of 70 cord blood samples were positive by nested PCR. These data suggest a high prevalence of infection among adult patients with long term, nonspecific complaints who live in close contact with animals and the possible existence of a chronic post-acute Q fever syndrome in Japan.