The aim of the present study was to compare the postoperative pain after the use of manual and rotary instrumentation of the same ProTaper Universal system (Dentsply Maillefer, Tulsa Dental, TN, USA) in a parallel randomized, controlled clinical trial.Forty-six patients with (vital and non-vital) mandibular posteriors (premolars and molars) without periapical radiolucencies underwent one visit root canal treatment. They were divided into two equal groups with 23 patients pear each, according to the instrumentation technique used group1 (manual protaper files) and group2 (rotary protaper files). Preoperative pain was recorded and postoperative pain was assessed after 6, 12, 24, 48, 72 hours and 7 days using the Visual Analogue Scale (VAS).Results showed that there was no statistically significant difference in the postoperative pain intensity between the two groups preoperatively, after 6 hours and 7 days, but after 12 hours group 2 showed higher prevalence of no pain and mild pain while group1 showed higher prevalence of moderate pain. After 24 and 48 hours group2 showed higher prevalence of no pain while group1 showed higher prevalence of mild pain and moderate pain, and after 72 hours showed higher prevalence of no pain while Group1 showed higher prevalence of mild pain.A very low incidence of severe pain was recorded for Group2 after 12 and 72 hours, which was 4.3%.Group2 showed lower pain intensity compared to group1 after 12, 24 and 72 hours postoperatively. Group 2 showed decrease in the pain intensity compared to preoperative pain, while group1 decrease in the pain intensity only after 48 and 72 hours. However, after 7 days significant decrease in the pain incidence (95.7% showed no pain) and pain intensity for both groups.There was no correlation between the postoperative pain and age, tooth type during all follow up periods, but male patients showed higher VAS scores compared to females at 12 and 72 hours. Also vital teeth showed higher VAS scores than the non vital teeth.Conclusion:Within the limitations of this study, the following could be concluded:1-Pain was less postoperatively after Rotary Protaper instrumentation.2-Pain decreases postoperatively by time.3-The least pain was encountered one week postoperatively in both groups.1-male patients showed higher VAS scores compared to females at 12 and 72 hours. Also vital teeth showed higher VAS scores than the non vital teeth.