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Objectives Literature shows that the expression of various biomarkers in peri-miniscrew crevicular fluid (PMICF) is related to the stability of miniscrew implants (MSIs). The present study investigated the role and alterations in levels of circulating cell-free nucleic acids (cfNAs) in PMICF before and after orthodontic loading. Material and methods This prospective study consisted of forty-six MSIs placed between the second premolar and first molar in the maxillary and mandibular arches. Direct loading was done after 3 weeks of MSI insertion with nickel-titanium closed coil spring exerting a force of 200 g. The PMICF sample was collected at various time intervals, and the level of cfNA was determined. Clinical parameters, including implant mobility and gingival health, were also assessed. Pre-loading and post-loading parameters were assessed using Wilcoxon’s rank-sum test. Results Among 46 MSIs, 36 were stable during the study and 10 MSIs showed peri-implant inflammation and increased mobility. There was a significant rise in the cfNA concentration 24 h after implant insertion (0.4 ± 0.86 ng/μl). The level of cfNAs significantly decreased over 3 weeks and reached the baseline level (0.2 ± 0.31 ng/μl). There was also a significant rise in the levels of cfNA (0.8 ± 0.70 ng/μl) at 24 h after loading MSIs, which gradually decreased to 0.2 ± 0.24 ng/μl after 63 days. The expression of cfNAs was on the average 0.32 units more in the cases with failed implants (P = 0.05). Conclusions cfNA levels in PMICF showed an upward trend 24 h after MSI insertion and 24 h after orthodontic loading. The expression of cfNA was more in cases with failed MSIs. Hence, the cfNAs can be considered as a prognostic biomarker of MSI stability.