Background: Acute encephalitic syndrome ( AES) is a complication of Scrub typhus(ST), an important re–emerging disease in India. In Japanese encephalitis(JE) endemic Assam, non JE AES cases remain under diagnosed and ST is likely to be an important but unsuspected etiology. Objectives: Study burden of AES due to ST in 7 districts of Assam reporting sporadic cases of ST. Methods: 246 samples from cases of AES found JE negative tested for ST IgM from February 2014 to December 2014 by enzyme–linked immunosorbent assay (ELISA). Results: 61 samples showed positive ST IgM ELISA accounting for 24.8%. Highest number of cases (31) seen in Lakhimpur district. All positive cases responded well to Doxycycline therapy. Conclusion: In Assam ST should be tested in all AES cases that are JE negative as ST involving central nervous system is not uncommon and it responds dramatically to Doxycycline therapy thus bringing down morbidity and mortality..