Introduction: In recent years, scrub typhus has rapidly emerged to become the major cause of acute febrile illness (AFI) in India. The commonest tests used for diagnosis are serology and PCR. Therefore, the present study was planned to compare these two techniques in the diagnosis of scrub typhus. Aim of the study: To compare IgM ELISA and PCR for diagnosis of scrub typhus as a causative agent of AFI. Material and Methods: Patients with acute undiagnosed febrile illness presenting to the outpatient (OPD) or inpatient services of PGIMER Chandigarh between August 2013 and March 2014 were included in this study. Blood was collected for further analysis by IgM ELISA and nested PCR followed by Sanger sequencing. Result: Of 176 patients, 29 (16.4%) were positive for scrub typhus by nested PCR while 162 (92%) were positive by IgM ELISA. There was 59 % concordance between the two tests. Conclusion: This study report shows that the concordance between PCR and ELISA for the diagnosis of scrub typhus is less than 60%. Ideally, both tests should be performed to diagnose scrub typhus depending on the day of presentation to hospital