BACKGROUND: Postoperative sore throat is a common complication of endotracheal intubation and can lead to dissatisfaction after surgery. Airway management has the strongest influence on the incidence of sore throat and improving endotracheal intubating conditions can reduce this complaint. Type of induction agent used during anesthesia can contribute to variances in the degree of post-operative sore throat. OBJECTIVES: We aimed to compare the incidence of postoperative sore throat after rapid sequence induction with Succinylcholine and high dose Cisatracurium. PATIENTS AND METHODS: The study was carried out on patients admitted to Shohada-e-Tajrish hospital for emergent abdominal surgery. Of the 80 patients who were enrolled in the study, 40 were randomly assigned to receive Succinylcholine while the remaining patients received Cistracurium during induction. Sore throat, muscle ache, hoarseness, dry throat and pain were assessed in each patient at baseline in recovery and at 2, 4, 12 and 24 hours post-operation. RESULTS: Number of patients who developed sore throat was significantly higher in the Succinylcholine group (75%) compared to Cisatracurium group (27.5%) at the time of entrance to the recovery room (P = 0.001). These numbers decreased at 2 hours post-operation (42% versus 17.5%) but the difference was still statistically significant (P < 0.05). At 12 (P = 0.062) and 24 (P = 0.14) hours post operation, the difference was no longer significant. CONCLUSIONS: Use of high dose Cisatracurium for induction during rapid sequence intubation carries a lower chance of developing sore throat compared to Succinylcholine. Studies comparing other adverse effects of these two agents are required to guide physician's choice of induction agent.