Objective. This study is aimed at determining (1) the effect of root-end resection, ultrasonic root-end preparation, and root-end filling on the incidence of crack formation and propagation by using a digital microscope (DM) and optical coherence tomography (OCT) and (2) the performance of OCT on the detection of cracks by comparing with microcomputed tomography (micro-CT) as a reference standard. Methodology. Thirty extracted lower incisors were endodontically treated and subjected to root-end resection and ultrasonic root-end cavity preparation. Then, the teeth were divided into three groups (n=10, each), and the root-end cavity was either left unfilled or filled with mineral trioxide aggregate (MTA) or super-EBA. The resected surface was observed with OCT and DM after the root-end resection, ultrasonic root-end preparation, and root-end filling, and the frequency of incomplete and complete cracks were recorded. The observation was repeated after two weeks, one month, and two months, and micro-CT scans after two months were taken as the gold standard. Results. The DM results show dentinal crack formation in 47% of the samples following root-end resection and in 87% following ultrasonic preparation. After the ultrasonic preparation, no existing crack propagated to a complete crack, but new cracks were formed. MTA and super-EBA had no effect on crack formation. The Spearman correlation coefficient between OCT and DM was 0.186 (very weak correlation; p=0.015). Sensitivity and specificity in comparison to micro-CT were 0.50 and 0.55 in OCT and 1.00 and 0.35 in DM, respectively. McNemar’s test showed a significant difference between OCT and DM (p<0.05). Conclusion. Apical resection and ultrasonic preparation could form dentinal cracks. OCT and DM showed different detection frequencies of cracks with very weak correlation. DM showed superior sensitivity compared with OCT.