Introduction <p>The objective of this study was to compare the quality of obturation in the mesial roots of mandibular molars with isthmuses, using Er, Cr: YSGG laser and sonic-activated irrigation, assessed by micro-CT scanning.</p> Methods <p>Mesial canals of extracted mandibular molars were instrumented to a master apical file size of 20/V06. The final irrigation protocol included 2.5% NaOCl, 17% EDTA, and a final rinse with 2.5% NaOCl, applied with either sonic-activated or laser-activated irrigation using the WaterLase iPlus (BIOLASE, Inc, Foothill Ranch, CA). Canals were obturated with Bioceramic Sealer HiFlow (Brasseler, Savannah, GA) and gutta-percha cones. Micro-computed tomography scans were obtained before and after obturation to evaluate the quality of obturation, determined by the percentage of unfilled spaces in each irrigation group.</p> Results <p>There was no statistically significant difference in baseline canal characteristics, including isthmus width, canal volume, root curvature, and Weine classification between the groups (<i>p</i> &gt; 0.05). In the post-obturation evaluation with micro-CT, the mean percentage of unfilled spaces was higher in the sonic group (17.24%) than in the laser group (10.73%), showing a statistically significant difference (<i>p</i> &lt; 0.05).</p> Conclusions <p>This study suggests that laser-activated irrigation may improve the quality of obturation in mandibular molars with isthmuses compared to sonic-activated irrigation.</p> Clinical significance <p>This study demonstrates that laser-activated irrigation can lead to a higher quality of obturation in conservatively instrumented canals by reducing the percentage of unfilled spaces. However, these findings should be cautiously interpreted, as the improved obturation quality observed may not directly translate to clinical outcomes. Further research is needed to determine if this advanteg influence long-term treatment success.</p>