ABSTRACT Background/Aims To evaluate the prevalence and timing of post‐operative complications following tooth autotransplantation, identify factors associated with earlier diagnosis, and report long‐term survival and success rates. Materials and Methods A single‐centre retrospective cohort study was conducted at a Czech university dental clinic (2003–2024); no external funding. Donor teeth were grouped as premolars, molars and anterior (canines, incisors, one premaxillary supernumerary; predominantly single‐rooted, single‐canal). Root development was classified according to Moorrees: early (1–3), optimal (4–5), late (6–7). Survival/success were estimated with Kaplan–Meier; timing of first diagnosis with event‐only cumulative incidence (1–Kaplan–Meier); and factors associated with earlier occurrence with Cox proportional hazards regression. Results The study included 134 teeth in 111 patients (74 premolars, 48 molars, 12 anterior). Half of the complications were diagnosed within 18 months (median time to first diagnosis: 11.7 months inflammatory resorption, 19.6 months apical pathology, 18.0 months cervical resorption, 21.4 months replacement resorption). Five‐year survival: premolars 95.4%; molars 86.6%; anterior 75.8%. Five‐year success: 75.3%, 76.8% and 66.0%, respectively. Age ≥ 30 years was associated with earlier tooth loss and apical pathology; male gender with earlier inflammatory resorption and loss of success. Anterior teeth and restorative indications (e.g., caries, previous root canal treatment failure) were associated with earlier apical pathology. A single preoperative dose of amoxicillin 1 g ~1 h before surgery or a 7‐day post‐operative amoxicillin course (500–1000 mg) was associated with delayed diagnosis of infection‐related complications. Some treated complications recurred or transformed into another type, requiring additional intervention. Conclusions Early detection enables successful management of most complications. As half occurred within 18 months—the critical window—follow‐up should include reviews at 1 week, 1 month, 3 months and every 3 months until 2 years post‐transplantation, with continued long‐term monitoring for recurrences and late complications.