AimThe purpose of this study was to quantify the effect of five different root canal preparation instruments on Substance P (SP), Calcitonin gene‐related peptide (CGRP) and their receptors expression in healthy human periodontal ligament.MethodologySTROBE guidelines were used to design a study using 60 periodontal ligament samples obtained from healthy lower premolars where extraction was indicated for orthodontic reasons. Prior to extraction 40 of these premolars were equally divided into four groups and root canals were prepared using different systems: Mtwo, Reciproc Blue, HyFlex EDM and Plex‐V. Ten premolars were prepared with hand files and served as a positive control group. The remaining 10 premolars where extracted without treatment and served as a negative control group. All periodontal ligament samples were processed to measure the expression of SP, CGRP and their receptors by radioimmunoassay. Kruskal–Wallis and Duncan tests were performed to determine statistically significant differences between the groups for each variable.ResultsGreater expression of all the peptides measured were found in the hand‐file preparation group, followed by the Reciproc Blue, Mtwo, HyFlex EDM and Plex‐V groups. The lower SP, CGRP and their receptors values were for the intact teeth control group. Kruskal–Wallis test showed statistically significant differences amongst groups (p < .001). Dunn post‐hoc tests showed statistically significant differences in SP, CGRP and their receptors expression between the intact teeth and the hand‐file and Reciproc Blue groups. Hand‐file group showed significant differences with the other groups, except with Reciproc Blue, where no differences were observed in any of the peptides measured. Finally, no differences were observed between Plex‐V and HyFlex in any of the peptides measured.ConclusionsRoot canal preparation with hand files and Reciproc Blue generates the highest expression of SP, CGRP, NK1 and CGRP1R in human periodontal ligament, whilst Plex‐V and HyFlex maintain the basal expression of neuropeptides and their receptors. Mtwo showed intermediate results between Reciproc Blue and HyFlex.