Background: Previous studies in medicine have demonstrated an inflation of outcome magnitude in clinical research related to bias. No studies have yet been conducted in oral health to investigate this effect. Objectives: To undertake a pilot study to investigate whether the magnitude of clinical outcomes in clinical trials in Periodontology is associated with the presence/absence of allocation concealment and examiner masking. Methods: Randomised controlled trials (RCTs) from the Cochrane Database of Systematic Reviews were searched to investigate the magnitude of clinical outcomes, using probing pocket depth and clinical/probing attachment level as outcome measurements. Methodological quality of the RCTs was then assessed in terms of allocation concealment and examiner masking. Meta-regression analyses were used to determine the associations between the quality assessments and magnitude of treatment outcomes. Results: Thirty-five RCTs were identified from five systematic reviews. Adequate allocation concealment and examiner masking was found in 24% and 64% of trials respectively. There were no statistically significant differences in the magnitude of treatment outcomes in trials in which allocation concealment was adequate, compared to those assessed as inadequate or unclear, nor were there any differences when comparing adequate and inadequately examiner masked trials. However, based on these data, a retrospective power calculation indicated the need for at least 265 RCTs to show a statistically significant difference of 0.5mm between groups with 80% power. Conclusions: There is insufficient evidence to support or refute the theory that the presence of allocation concealment and examiner masking affect the magnitude of clinical outcomes in this sample of RCTs. The current pilot data provide an essential baseline for sample size calculations for future research.