Scrub typhus, caused by Orientia tsutsugamushi, is a common cause of acute undifferentiated febrile illness in the Asia-Pacific region. However, its nonspecific clinical manifestation often prevents early diagnosis. We propose the use of PCR and serologic tests as diagnostic tools. Here, we developed a multiplex real-time PCR assay using hydrolysis (TaqMan) probes targeting O. tsutsugamushi 47-kDa, groEL, and human interferon beta (IFN- gene) genes to improve early diagnosis of scrub typhus. The amplification efficiency was higher than 94%, and the lower detection limit was 10 copies per reaction. We used a human gene as an internal DNA quality and quantity control. To determine the sensitivity of this PCR assay, we selected patients with confirmed scrub typhus who exhibited a clear 4-fold increase in the level of IgG and/or IgM. The PCR assay result was positive in 45 of 52 patients, indicating a sensitivity of 86.5% (95% confidence interval [CI]: 74.2 to 94.4). The PCR assessment was negative for all 136 non-scrub typhus patients, indicating a specificity of 100% (95% CI: 97.3 to 100). In addition, this test helped diagnose patients with inconclusive immunofluorescence assay (IFA) results and using single blood samples. In conclusion, the real-time PCR assay proposed here is sensitive and specific in diagnosing scrub typhus. Combining PCR and serologic tests will improve the diagnosis of scrub typhus among patients presenting with acute febrile illness.KEYWORDS Orientia tsutsugamushi, real-time PCR, scrub typhus S crub typhus is a mite-borne infectious disease caused by the obligate intracellular bacterium Orientia tsutsugamushi. A characteristic feature of the disease is patients presenting nonspecific symptoms, including fever, headache, myalgia, cough, and abdominal pain, which cannot be differentiated from symptoms of other systemic infections. The presence of eschar can help diagnose this illness; however, it is found only in some patients (1). Although the clinical course of scrub typhus is usually mild and self-limiting, delaying the treatment in severe cases can lead to complications such as renal failure, myocarditis, meningoencephalitis, and death (2). Since scrub typhus is one of the most common causes of acute undifferentiated febrile illness (AUFI) in areas of endemicity (3, 4), an early, definite diagnosis is essential for providing appropriate treatment and gathering accurate epidemiological data.Scrub typhus diagnosis mainly relies on serologic tests, particularly the indirect immunofluorescence assay (IFA), whereby the illness is identified by a 4-fold increase in antibody titers in paired sera (5, 6) and/or a positive IgM titer in a single serum sample (7,8). However, these serologic tests require paired serum samples and good technician expertise, and even then they often return false negatives during the early phase of disease. In addition, reinfection by different O. tsutsugamushi strains is not uncommon in areas of endemicity and reinfected patients may sometimes