The use of 3D intraoral scanners (IOS) and software that can support automated detection and objective monitoring of oral diseases such as caries, tooth wear or periodontal diseases, is increasingly receiving attention from researchers and industry. This study clinically validates an automated caries scoring system for occlusal caries detection and classification, previously defined for an IOS system featuring fluorescence (TRIOS 4, 3Shape TRIOS A/S, Denmark). Four algorithms (ALG1, ALG2, ALG3, ALG4) are assessed for the IOS; the first three are based only on fluorescence information, while ALG4 also takes into account the tooth color information. The diagnostic performance of these automated algorithms is compared with the diagnostic performance of the clinical visual examination, while histological assessment is used as reference. Additionally, possible differences between in vitro and in vivo diagnostic performance of the IOS system are investigated. The algorithms show comparable in vivo diagnostic performance to the visual examination with no significant difference in the area under the ROC curves ([Formula: see text]). Only minor differences between their in vitro and in vivo diagnostic performance are noted but no significant differences in the area under the ROC curves, ([Formula: see text]). This novel IOS system exhibits encouraging performance for clinical application on occlusal caries detection and classification. Different approaches can be investigated for possible optimization of the system.