Current study aimed to evaluate presence & concentration of salivary molecular pain biomarkers Calcitonin Gene Related Peptide (CGRP) and Brain-Derived Neurotrophic Factor (BDNF) during initial stages of orthodontic treatment and correlation with subjective pain scales, Numerical Rating Scale (NRS), Visual Analogue Scale (VAS), Verbal Rating Scale (VRS) and McGill Pain Questionnaire (MPQ). Consented, healthy-pain free patients (n = 40) undergoing orthodontic therapy, having moderate crowding with pre-molar extraction were recruited. Unstimulated whole saliva was collected and stored at -80 °C in cryotubes. Levels of CGRP & BDNF in salivary samples was assessed by enzyme–linked immunosorbent assay. Samples were collected under stipulated 5 time periods using saliva collection tube by passive drooling method: immediately after bonding but before wire placement (T0-baseline), after 24 h (T1), 48 h (T2), 72 h (T3) & 168 h (T4) after wire placement. Consolidated subjective pain scales were administered concurrently. Regression value (R2 > 0.9) confirmed BDNF & CGRP in saliva. Significant change was observed from baseline to 168 h in all subjective parameters (p < 0.05). CGRP did not correlate with subjective pain scales statistically (p > 0.05). BDNF levels correlated with all the subjective pain scales, NRS (T3-p = 0.0092&T4-p = 0.0064), VRS (T3-p = 0.0112&T4-p = 0.0500), VAS (T3-p = 0.0092 &T4-p = 0.0064) &MPQ (T1-p = 0.0255). Mean BDNF & median subjective pain scale graphs were similar. BDNF correlated with all the subjective pain scales warranting further investigation.Trial registration; Clinical Trial Registry—India (CTRI) Reg No: CTRI/2018/12/016571; Registered 10th December, 2018 (10/12/2018) prospectively; http://ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=29640&EncHid=&userName=Dr%20Sagar%20S%20Bhat.