OsBAT1 is homologous gene of human leukocyte antigen-B associated transcript 1 (BAT1) isolated from rice. It is also called as UAP56, which is a DExD/H-box protein involved in messenger RNA (mRNA) splicing. The function of plant homologue of BAT1, isolated from rice (OsBAT1) especially its involvement in stress tolerance, has been reported in T1 and T2 generation. Here, we demonstrate the novel function of OsBAT1 in salinity stress tolerance in rice (Oryza sativa L. cv. IR64) in T₃ generation. Rice over expressing OsBAT1 (T₃ generation) showed tolerance to high salinity (200 mM NaCl) stress. The T₃ transgenics exhibited higher levels of biochemical parameters such as water and chlorophyll contents, net photosynthetic rate, stomatal conductance and intercellular CO₂ content as compared to wild type (WT) plants. Agronomic parameters were also higher in transgenics as compared to WT plants. Our results provide the first direct evidence for a promising function of OsBAT1 in mediating salinity stress response/tolerance in rice and its stability up to T₃ generation.