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Flexible endoscopes are used in many diagnostic exams, like gastroscopies or colonoscopies, as well as for small surgical procedures. Recently, they have also been used for endoscopic surgical procedures through natural orifices [natural orifice transluminal endoscopic surgery (NOTES)] and for single-port-access abdominal surgery (SPA). Indeed, flexible endoscopes allow access of operating areas that are not easily reachable with only one small external or internal incision. However, their manipulation is complex, especially for surgical interventions. This study proposes to motorize the flexible endoscope and to partly robotize its movements in order to help the physicians during such interventions. The paper explains how the robotized endoscope can be used to automatically track an area of interest despite breathing motion. The system uses visual servoing and repetitive control strategies and allows stabilization of the endoscopic view. All required parameters are automatically estimated. In vivo experiments show the validity of the proposed solution for the improvement of the manipulation of flexible endoscopes.