This study set out to evaluate the prevalence of iatrogenic events during preclinical teaching of endodontics, comparing manual stainless steel versus nickel-titanium (Ni-Ti) rotary techniques for shaping natural root canals. Two groups of 13 inexperienced dental students were randomly made up and asked to shape 104 canals in natural teeth. Group R used Ni-Ti rotary files for shaping while Group M used a sequence of five manual stainless steel files. Occurrence of file breakage, loss of work length, and iatrogenic instrumentation on apical foramina were evaluated. Overall occurrence of adverse events during shaping did not differ between the groups, being 58% in Group R and 51% in Group M. Inter-group distribution of type of event differed significantly, however. File breakage (7.7%) and loss of working length of > 2 mm (6.7%) occurred only in Group R. Iatrogenic shaping on apical foramina showed the same frequency in each group. Manual instrumentation is safer than rotary instrumentation in the hands of inexperienced students. Acquiring skill in the use of Ni-Ti rotary instrumentation requires specific preclinical training to avert file breakage. These findings argue for the rethinking of theoretical and practical coursework in endodontics teaching, especially in dentistry schools where students are required to treat patients during their training.