Background <p>Dental students must master endodontic anatomy, radiographic diagnostics, and treatment strategies early in their clinical training—yet traditional teaching methods, including two-dimensional radiographs, often fail to effectively convey complex spatial structures. Hologram technology has emerged as a promising tool for three-dimensional visualization in dental education. The aim of the study was to compare the classification accuracy of dental students using holograms versus conventional periapical radiographs in identifying endodontic structures.</p> Methods <p>This randomized single center-controlled trial included 79 dental students (years 4–6). After a calibration seminar and pre-test each of the 79 students assessed six tooth cases—three presented as holograms and three as periapical radiographs. Holograms were created from cone-beam computed tomography data, annotated by two calibrated examiners to establish reference points regarding the number of canals, Vertucci classification, and treatment complexity. Students evaluated each case for these parameters; responses were compared to the reference points to assess classification accuracy. The final evaluation form captured their subjective perceptions of the new hologram system. Primary binary outcomes were analyzed using logistic mixed-effects models. <i>P</i>-values were adjusted for multiple testing using the Benjamini–Hochberg procedure. Statistical significance was set at <i>p</i> &lt; 0.05.</p> Results <p>After Benjamini–Hochberg correction, holography significantly improved root-canal number identification in three multi-rooted cases (adjusted <i>p</i> ≤ 0.007). For Vertucci classification, only the maxillary anterior tooth remained significant (adjusted <i>p</i> = 0.044). Treatment-complexity assessment showed case-dependent results, favoring radiography in two cases (adjusted <i>p</i> = 0.045 and <i>p</i> = 0.006) and holography in one case (adjusted p = 0.013).</p> Conclusions <p>Holographic visualization demonstrated case- and task-specific effects in endodontic training. Holograms were able to improve classification accuracy in certain endodontic tasks. However, they did not outperform conventional periapical radiographs in all outcomes. Holography could be an effective, supplementary tool for teaching certain endodontic tasks, but its application requires further investigation.</p> Trial registration <p>The study was prospectively registered in the German Clinical Trials Register (DRKS-ID: DRKS00035000) on 13.09.2024.</p>