Tuberculosis (TB) has emerged as one of the leading health problem since last three decades. High rate emergence of extremely multiple drug resistant Mycobacterium strains results in inefficiency of available prophylactic and therapeutic means. Hence there is an urgent need to search for alternative, safe, effective and affordable preventive as well as therapeutic strategies against TB. ESAT-6 is an early secreted protein by Mycobacterium tuberculosis that can be used as target for efficient peptide vaccine design against TB. In present study, initially new epitopes were identified using online epitope prediction tools and structural models of both ESP-1 and ESP-6 epitopes derived from ESAT-6 were developed. Later on these epitopes were used for molecular dynamics analysis. Results obtained from molecular dynamics analysis on ESP1 and ESP6 epitopes direct need to focus further study on their interaction with MHC molecules.