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Background: The development of calcium silicate materials and new techniques have resulted in significant clinical benefits in endodontics and microapical surgery. The objective of this investigation was to analyze the percentage of dentinal tubule penetration of two retrograde obturation techniques in microapical surgery, namely the conventional technique and the lid technique. Methods: 60 single-root human teeth were selected, which were divided into two groups (n = 30). These teeth were subjected to an endodontic procedure using the single-cone technique. They were prepared with apicoectomy and 3 mm apical retrocavity and then obturated using two retrograde obturation techniques with bioceramic materials: TotalFill RRM fast set Putty^® (RRM) using the conventional technique and TotalFill BC Sealer HiFlow^® (HiFlow) and RRM using the lid technique. The teeth were selected and evaluated using 1 mm portions in the apical third. In each case, the images were obtained using a Leica TCS SP8 Confocal Microscope (CLSM). The extent of penetration into the dentinal tubule regions was measured using AutoCad^®. Results: Statistical analyses were performed using the Levene test (p ≤ 0.05) and Student’s t-test (p ≤ 0.05). Analysis of the penetration area of calcium silicate materials into the dentinal tubules revealed that the relative penetration percentages were higher when using the conventional technique with the RRM than the lid technique with RRM + HiFlow in the apical third evaluated. Conclusion: The conventional technique yields significantly better outcomes, showing statistically significant differences in the percentage of penetration into the intratubular area compared to the lid technique. Full article