Background: Recently, it has been suggested that azithromycin (AZM) may be a useful adjunct to non-surgical periodontal therapy (NSPT). However, current scientific evidence is still not conclusive as to its efficacy as an adjunct of NSPT. This study aimed to evaluate the effect of the systemic administration of AZM as an adjunct to NSPT on the clinical and microbiological variables of patients with periodontitis.Methods: Eighteen volunteers with Periodontitis received NSPT combined with placebo or AZM (500 mg/day) for 3 days (n=9/group). They were monitored clinically for probing pocket depth (PPD), clinical attachment level (CAL), plaque index (PI) and bleeding on probing (BoP) at baseline and during the first, third and sixth month and monitored microbiologically at baseline and at 3 and 6 months after therapy. The microbiological variables were detected by conventional polymerase chain reaction tests. The normality was checked using the Shapiro-Wilk test. The level of statistical significance was measured by the unpaired t-test, Mann-Whitney U, Fisher’s exact and Chi-Square tests.Results: Fourteen patients completed the study (n=7/group). The group receiving NSPT + AZM presented with a significantly lower mean PPD at 3 (p = 0.05) and 6 months (p = 0.04) with a greater probing depth reduction (p = 0.02). Moreover, at the third month post NSPT, there was a significant increase in the number of sites with a PPD 1–3 mm (p < 0.001) and a decrease in the number of sites with a PPD 4–6 mm (p < 0.001). In addition, a significant decrease in the mean number of sites with a PPD ≥ 7 mm (p = 0.04) was detected at 6 months post treatment. There was also a significant decrease in BoP at 1 (p = 0.01), 3 (p < 0.001) and 6 (p = 0.01) months post intervention. Conclusions: AZM as an adjuvant to NSPT provides additional beneficial effects for PPD and BoP compared to NSPT alone. This could be related to its anti-inflammatory properties more than to its antibiotic characteristics.Trial registration: ClinicalTrials.gov: NCT03629288. https://clinicaltrials.gov/ct2/show/NCT03629288Retrospectively registered on August 14, 2018.