Background: IL-13 is the key cytokine in the regulation of inflammatory with an autoimmune disease and has an anti-inflammatory effect. Aims: This study aimed to compare IL-13 (-1112 C/T and -1512 A/C) gene polymorphisms in patients with aggressive periodontitis (AgP), chronic periodontitis (CP), and periodontally healthy group (C) and evaluate the effect of nonsurgical periodontal therapy on gingival crevicular fluid (GCF) IL-13 levels in patients. Materials and Methods: One hundred thirty patients with AgP, 120 patients with CP, and 70 periodontally healthy subjects were included in this study. Clinical parameters were recorded (plaque and gingival index, probing pocket depth, clinical attachment level), and GCF and blood samples were taken at baseline and 6-week. Nonsurgical periodontal therapy was performed in patients with periodontitis. Gene analyses (IL-13 - 1112C/T (rs1800925) and - 1512 A/C (rs1881457) were performed with real-time polymerase chain reaction (PCR) and cytokine levels were determined by an enzyme-linked immunosorbent assay method. Results: AgP and CP patients showed significant improvement in clinical parameters after periodontal therapy (P < 0.05). According to results, genotype distributions and allele frequencies in IL-13 variants - 1112C/T and - 1512 A/C were found similarly in all groups (P > 0.05). In the AgP group, GCF IL-13 cytokine level is statistically significant and increased in 6 weeks; however, in the CP group, there is no statistically significant difference between baseline and 6 week. In the AgP group, baseline GCF IL-13 cytokine level is lower than those of the CP group and C group (P < 0.05). Conclusion: Within the limits of this study, IL-13 -1112 and -1512 gene polymorphisms have not been associated with AgP and CP, and GCF IL-13 cytokine level is increased after treatment in the AgP group.