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Background: Eccentric instruments have been proposed as more effective and less time-consuming for endodontic instrumentation., Aim: To compare biomechanical outcomes of different instrumentation systems and time undertaken for instrumentation in resin prototypes., Design: Sixty standardized prototypes of mandibular second primary molars were instrumented according to the following systems: K-files, ProTaper Next (PTN), XP-endo Shaper (XPS), XP-endo Finisher (XPF), XP-Clean (XPC), and Sequence Baby File (SBF; n = 10/each). Irrigation was performed with saline with simultaneous aspiration, and time spent was recorded. The prototypes were micro-CT-scanned before and after the instrumentation, and image sets were reconstructed and registered. Non-instrumented areas, accumulated debris, removed root material volume, and canal transportation were quantified. Data were analyzed through ANOVA, the Kruskal-Wallis test, and the Wilcoxon signed-rank test (α = 5%)., Results: K-files and SBF resulted in more instrumentation time (p < .05). SBF, XPC and PTN removed less root dentine (p < .05), but PTN left more untouched areas (p < .05). Accumulated debris were lower for XPC and SBF (p < .05). Canal transportation was similar among the groups., Conclusion: Rotary systems reduced instrumentation time, whereas SBF and XPC resulted in more conservative instrumentation, with less debris accumulation and non-instrumented areas. A dedicated paediatric endodontic system (SBF) outperformed eccentric instruments in terms of effectiveness., (© 2023 BSPD, IAPD and John Wiley & Sons Ltd.)