In this retrospective study, it was investigated whether the use of a fifth-generation rotary system (ProTaper Next) resulted in improved radiological root filling quality compared to a first-generation counterpart (ProFile) in a controlled student course setting. Cases treated by fourth-year dental students in the 2020/21 academic year were collected and compared to those treated in 2019/20. Root canals in the former group were all instrumented using the ProTaper Next system, and the latter using the ProFile system. All other clinical parameters were similar between the two academic years, including the time of pre-clinical teaching, hands-on course hours, endodontic auxiliaries, and chemicals used for treatment. After excluding patients who were not available or refused to give their informed consent to this study (n = 20), and excluding teeth with missing or poor radiographs (n = 16), the fillings in 178 roots could be assessed by two calibrated observers blinded to the system that was used. The primary outcome was the radiographic quality of the root fillings according to the five-scale modified MOLANDER score. The secondary outcome was the number of separated rotary instruments by group. Both instrumenting systems resulted in a similar number of "excellent" root fillings (score I), 59 % in the ProTaper Next group and 60% in the ProFile group, with no statistically significant difference in outcome scores between groups (Probability > ChiSquare = 0.70). Furthermore, there was merely one separated instrument in the ProTaper Next group, and none in the ProFile group (Fisher's exact test, p = 1.00).