Objectives <p>This study aimed to compare the periodontal status of periodontally healthy individuals with those of smokers and non-smokers with stage 3 periodontitis before and after treatment, as well as to investigate the levels of Gremlin-1, Syndecan-4, and IL-1β in GCF samples. Another objective of the study was to evaluate the relationship between these biomarkers and periodontitis and to assess the effects of smoking on their levels.</p> Materials and methods <p>A total of 45 volunteers, 15 smokers (Group SP) and 15 non-smokers (Group NP) diagnosed with stage 3 periodontitis between the ages of 18 and 60, and 15 healthy individuals (Group H) were included in the study.</p> Results <p> All clinical parameters of the SP and NP groups were found to be significantly higher than those of the H group before NSPT (<i>p</i>&lt;0.001), and a significant reduction was observed in all clinical parameters after phase I treatment (<i>p</i>&lt;0.001). Following NSPT, significant improvement was observed in all periodontal parameters in both periodontitis groups (<i>p</i>&lt;0.001). Gremlin-1 levels in the SP and NP groups were statistically significantly lower after treatment compared to pre-treatment levels (p&lt;0.05). While there was no statistically significant difference in IL-1β levels before and after treatment in the SP group (<i>p</i>&gt;0.05), a statistically significant reduction was observed in the NP group after treatment (<i>p</i>&lt;0.05). Similarly, no statistically significant difference was found in Syndecan-4 levels before and after treatment in the SP group (<i>p</i>&gt;0.05), whereas the post-treatment measurements of the NP group were statistically significantly lower (<i>p</i>&lt;0.05).</p> Conclusions <p> After NSPT, Gremlin-1 levels in GCF decreased in both groups, whereas significant reductions in Syndecan-4 and IL-1β levels were observed only in non-smokers. These findings suggest that the regulatory effect of smoking on biomarkers may negatively influence the periodontal treatment response.</p> Clinical relevance <p> Smoking is a major risk factor for periodontitis and may impair healing following nonsurgical periodontal therapy. While similar clinical improvements were observed, reductions in IL-1β and Syndecan-4 occurred only in non-smokers, whereas Gremlin-1 decreased in both groups. These findings suggest that smoking may influence molecular healing responses, and biomarker monitoring may support personalized periodontal management.</p>