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Abstract A randomized clinical trial to compare the effect of reciprocating single-file to rotary instrumentation on the intensity of post-operative pain and the level of endotoxins in primarily infected root canals. Forty patients having necrotic mandibular molar teeth with apical periodontitis were randomly assigned into two groups according to the instrumentation system used; control group: ProTaper Next group (PTN) and intervention group: WaveOne group (WO). Preoperative pain was recorded using numerical rating scale (NRS). Root canal treatment was performed on two visits. In the first visit, after isolation and disinfection, access cavity was performed followed by chemico-mechanical preparation which was done using PTN in the control group and WO in the intervention group with 2.5% NaOCl irrigation. Then, intracanal medication was placed. One week later, removal of intracanal medication and root canal obturation were performed. Postoperative pain was recorded at 6, 12, 24 and 48 hours after both instrumentation and obturation visits. Endotoxin samples were collected by three paper points immediately after access cavity preparation (S1) and after chemico-mechanical preparation (S2). A sandwich ELISA method was used for the quantification of endotoxins |