Aim of the study: The aim of the present randomized clinical study was to evaluate the effect of OneShape and Protaper Next rotary system on the removal of endotoxins from teeth with asymptomatic necrotic pulp.Materials and Methods: Thirty patients were randomly allocated into two groups (n=15) according to the type of rotary system used in mechanical preparation; either Group OS (OneShape) or Group PN (Protaper Next). Samples were taken before and after mechanical preparation and quantification of endotoxins was done using Human Elisa kit. Statistical analyses were performed using Mann-Whitney U test to compare between the two groups then Wilcoxon signed- rank test was used to study the changes after treatment within each group. The significance level was set at P ≤ 0.05.Results: Group OS, showed a statistically significant reduction in endotoxins levels after treatment (P-value < 0.001, Effect size = 0.880). In Group PN, there was a statistically significant reduction in endotoxins levels after treatment (P-value <0.001, Effect size = 0.931) and Group OS showed statistically significant lower median % reduction in endotoxins level than Group PN.Conclusion: Protaper Next was more effective than the Oneshape in reducing the endotoxins from teeth with asymptomatic necrotic pulp.