The aim of this in vitro study was to systematically investigate new caries diagnostic tools, including three intraoral scanners, and compare them to established diagnostic methods. For a standardized analysis of occlusal and proximal caries lesions, human permanent and primary teeth (n = 64) were embedded in models and investigated in a phantom head using six different caries diagnostic methods: visual examination, bitewing radiography, Diagnocam (KaVo, Biberach, Germany), Trios 4 (3Shape, Copenhagen, Denmark), iTero Element 5D (Align Technology, San José, CA, USA), and Planmeca Emerald S (Planmeca, Helsinki, Finland). The diagnostic methods were investigated and compared to reference µ-CT for permanent and primary teeth separately. For occlusal caries diagnostics in permanent teeth, the best agreement to the reference (reliability) was obtained for Planmeca Emerald S (ĸ = 0.700), whereas in primary teeth, for visual examination (ĸ = 0.927), followed by Trios 4 (ĸ = 0.579). Regarding proximal caries diagnostics, bitewing radiography, as the gold standard, exhibited the highest agreement for permanent (ĸ = 0.643) and primary teeth (ĸ = 0.871). Concerning the analysis of the diagnostic quality (sensitivity and specificity) using receiver operating characteristic (ROC) curve analysis, comparable findings were obtained for area under curve (AUC) values as for reliability. No diagnostic method could be identified that is generally suitable for occlusal and proximal lesions in both dentitions. Overall, caries diagnostics with intraoral scanners seem to be interesting tools that should be further investigated in clinical studies.