We assessed the clinical usefulness of immunohistochemical staining on skin biopsy specimens for the diagnosis of scrub typhus compared with indirect immunofluorescent antibody assay (IFA), the definitive diagnostic method for scrub typhus, in a prospective study of 125 patients with possible scrub typhus in 2005 and 2006. Skin biopsy specimens were obtained from 63 patients. To minimize the effects caused by antibiotics on immunohistochemical results, 46 patients were assessed before antibiotic administration (4 patients received antibiotic therapy before admission; 13 underwent skin biopsy after antibiotic administration at our hospital). Compared with IFA results, immunohistochemical results on maculopapular skin lesions demonstrated a sensitivity of 0.65 and a specificity of 1. Immunohistochemical results on eschars demonstrated a sensitivity of 1 and a specificity of 1. For immunohistochemical staining performed on skin lesions within 3 or 4 days of administration of antibiotics that are effective for Rickettsia, the antibiotics did not greatly influence diagnostic sensitivity. Immunohistochemical staining of skin biopsy specimens, particularly that of eschars, is sensitive and specific, and this technique can be reliable for confirming the diagnosis of scrub typhus.