Background <p>Intra-oral scanners (IOS) have been widely used to obtain digital impressions for treatment planning and to enable a full digital workflow on virtual patients. Much less is known about the use of IOS for caries detection. This study focuses on the use of the scanners for caries detection and investigates the number of images, time and patient experiences as well as differences between operators.</p> Methods <p>Participants were recruited if they had caries present, their teeth were cleaned using a prophy brush and water and then scanned in a standardised manner. Some participants were scanned a second time by another operator. The automated caries detection results as well as the number of images needed and time taken per jaw scanned was noted. Participants were also asked to complete a questionnaire regarding their experience during the scanning process.</p> Results <p>Data sets (scanning time and number of images) from 78 participants were both found to be non-normal using the Shapiro Wilk test (<i>p</i> &lt; 0.001). A Mann-Whitney U test revealed that both the time taken (U = 17772.500, z = -8.066, <i>p</i> &lt; 0.001) as well as the number of images needed (U = 15252.000, z =-9.651, <i>p</i> &lt; 0.0001) were significantly higher for the maxilla when compared to the mandible. The same test also showed that significantly more time (U = 102718.500, z = 14.505, <i>p</i> &lt; 0.0001) and images (U = 108395.500, z = 16.457, <i>p</i> &lt; 0.0001) were needed for scanning permanent teeth when compared to primary teeth. The questionnaire revealed that the vast majority of participants (87%) found the scanning procedure comfortable and acceptable but there were statistically significant differences in discomfort experienced in different areas of the mouth, with the most uncomfortable area scanned being the distal surfaces of the upper molars (<i>p</i> &lt; 0.001). A Wilcoxon Signed Rank test revealed no significance difference in jaw scanning time (z = 0.118, <i>n</i> = 12, <i>p</i> = 0.906) and number of images taken per arch (z = 1.255, <i>n</i> = 12, <i>p</i> = 0.209) between the operators. Cohen’s Weighted Kappa yielded the following significant result: κ = 0.744, <i>p</i> &lt; 0.0001 showing good agreement between the operators’ automated caries detection results.</p> Conclusions <p>Intra-oral scanning is well-accepted by patients even when used for caries detection. This scanner also yields similar results for different operators which makes it a reliable tool.</p> Trial registration <p>Not applicable.</p>