Aim: To investigate, by means of multilevel analysis, factors that may affect the short‐term clinical outcome of non‐surgical periodontal treatment.

Materials and Methods: Forty‐one patients randomly assigned to two protocols of non‐surgical therapy were included. The impact of different covariates on the probability of “pocket closure” [i.e. probing pocket depth (PPD)4 mm] was explored using a logistic multilevel model. The impact on the final PPD was explored using a continuous multilevel model.

Results: The logistic model revealed a significant impact of smoking (p<0.001), presence of plaque at the site (p<0.001) and location of the pocket at a multi‐rooted tooth (p<0.001). The model explained 44% of the total variability. Of the unexplained variance, 19% was attributed to inter‐patient variability. The continuous model revealed the same factors to be significant and an additional significant impact of interactions between the covariates. The R² was 0.50 and the random slopes model revealed an increase in the variability of the final pocket depth with an increase in the initial PPD.

Conclusion: Smoking habits, plaque at site level and tooth type were significant factors in determining the short‐term clinical outcome of non‐surgical periodontal treatment.