Abstract Objectives Individual orthodontic treatment duration is hard to predict. Individual biological factors are amongst factors influencing individual rate of orthodontically induced tooth movement (OTM). The study aim is to determine the rate of OTM by a novel 3D method and investigate parameters that may predict the rate of tooth movement. Materials and methods In this prospective cohort study, rate of OTM was determined from 90 three-dimensional intra-oral scans in 15 patients (aged 12–15) undergoing orthodontic treatment. For each patient, intra-oral scans were taken every week for up to 6 weeks (T0–T5). The teeth were segmented from the scans and the scans were superimposed on the palatal rugae. The rate of OTM was calculated for each tooth. Other parameters were gingival inflammation, contact-point displacement and the biological markers, matrix metalloproteinases (MMP), MMP-9 and MMP-2 in gingival crevicular fluid (GCF). Results Our study showed a high variation in the rate of OTM, varying from 0.15 to 1.24 mm/week. Teeth in the anterior segment tended to move more compared with the posterior segment. The contact point displacement and gingival inflammation varied greatly amongst the patients. The MMPs measured did not correlate with tooth movement. However, the gingival inflammation index showed a significant correlation with OTM. Future studies should include other biological markers related to bone-remodeling. Conclusion This novel and efficient 3D method is suitable for measuring OTM and showed large individual variation in rate of OTM. Clinical relevance Patients show different rates of OTM. The rate of OTM in an individual patient can provide guidance in timing of follow-up appointments.