The aims of the present study were to determine the levels of vaspin and omentin-1 in gingival crevicular fluid (GCF) in patients with chronic periodontitis (CP) with and without type 2 diabetes mellitus (T2DM), and to evaluate GCF vaspin and omentin-1 levels after non-surgical periodontal therapy. The study included 60 subjects: 15 systemically and periodontally healthy individuals, 15 periodontally healthy patients with T2DM, 15 systemically healthy patients with CP, and 15 patients with both CP and T2DM. GCF and clinical periodontal parameters were examined at the baseline and 6 weeks after periodontal therapy. Levels of vaspin, omentin-1 and tumor necrosis factor-alpha (TNF-alpha) were measured by ELISA, and their relative ratios were calculated. GCF vaspin and TNF-alpha levels were significantly higher in the CP groups than in the periodontally healthy groups (P < 0.008) and decreased after therapy in the former (P < 0.025). GCF omentin-1 levels were significantly lower in the CP groups than in the periodontally healthy groups (P < 0.008) and increased after therapy in the former (P < 0.05). Statistically significant positive correlations were found between the total amount of vaspin and TNF-alpha, glycated hemoglobin (HbA1c), clinical attachment level and gingival index, whereas the level of omentin-1 was negatively correlated with these parameters in all groups (P < 0.05). We found that non-surgical periodontal therapy influenced the GCF levels of both vaspin and omentin-1 in the CP groups. Our results suggest that the levels of vaspin and omentin-1 in GCF could have potential application as inflammatory markers of diabetes, periodontal disease and treatment outcome.