The aims of this study were to determine the diagnostic accuracy and clinical usefulness of using nested polymerase chain reaction (PCR) for the diagnosis of scrub typhus through a prospective comparison of nested PCR and indirect immunofluorescent antibody assay (IFA). We conducted a multi-center prospective study of patients who were suffering with possible scrub typhus infection. Whole blood samples were collected for PCR testing, and sera were obtained for serology evaluation using the indirect IFA and the passive hemagglutination assay (PHA). We prospectively studied 135 patients with possible scrub typhus. One hundred eighteen patients were confirmed as having scrub typhus, 7 patients were undetermined, and 10 patients were confirmed as having other diseases. The results of nested PCR assay showed a sensitivity of 82.2% and a specificity of 100%. Ninety-six of the 118 patients were positive for IgM on their admission day. Of the 22 patients who were negative for IgM antibody at admission, 19 had positive results for nested PCR of the buffy coat. The nested PCR assay of the buffy coat is useful as a rapid and reliable test for confirming the diagnosis of scrub typhus.