We performed a case-control association study to identify risk SNPs at major DSB repair (RAD50, MRE11A, NBS1, PRKDC, XRCC5, XRCC6 and LIG4), MMR (MSH6 and MSH3) and key DNA damage response (ATM and ATR) genes in oral cancer and leukoplakia patients from the state of West Bengal of eastern India. This evidence concerns the gene MSH3 and leukoplakia.