Background: Mucoperichondrial flap elevation is the first step in septoplasty operation. MESNA was used in flap elevation to decrease the amount of bleeding, get better surgical field, decrease the operation time and lessen mucosal damage. Objectives: To evaluate the effect of submucosal injection of sodium 2- mercaptoethanesulfonate  (MESNA) on the operation time, intra-operative blood loss, integrity of the flap in septoplasty and post operative pain. Patients and methods: It is a case control study that was conducted on 60 patients their ages ranged from 18 years to 43 years, all were underwent septoplasty operation by the  same surgeon at Otorhinolaryngology Department, Qena University hospitals, Egypt. Results: Results revealed that the mean time of flap elevation was 6.7±1.8 SD minutes in group A, but was 10.9 ± 2.2 SD minutes in group B which was highly statistical significant with p-value < 0.001.As regard the mean of Intra-operative blood loss it was82 ±15.9 SD ml. in group A, but was 109.7 ± 21.8 SD ml. in group B which was highly statistical significant with p-value < 0.001. Conclusion: Submucosal injection of sodium 2- mercaptoethanesulfonate (MESNA) being  more advantageous method that  make mucoperichondrial flap elevation is convenient and effective and preserving mucosal integrity in surgical treatment of deviated nasal septum .