Purpose: To investigate the correlation between periodontal parameters and cell-free DNA (cfDNA) concentrations in gingival crevicular fluid (GCF), saliva, and plasma. Methods: Full mouth periodontal parameters, including probing depth (PD), bleeding on probing (BOP), and plaque index (PI) were recorded from 25 healthy volunteers, 31 patients with untreated gingivitis, and 25 patients with untreated periodontitis. GCF, saliva, and plasma samples were collected from all subjects. Extraction and quantification assays were undertaken to determine cfDNA concentrations of each sample. Results: GCF and salivary cfDNA levels were increased with aggravation of periodontal inflammation (GCF p < 0.0001; saliva p < 0.001). Plasma cfDNA concentrations in patients with periodontitis were significantly higher than those in healthy volunteers and patients with gingivitis. GCF and salivary cfDNA were positively correlated with mean PD, max PD, BOP, and mean PI (p < 0.0001), whereas plasma cfDNA was not correlated with BOP (p = 0.099). Conclusion: GCF, saliva, and plasma concentrations of cfDNA were significantly elevated in patients with periodontal disease. There were also positive correlations between cfDNA levels in GCF and saliva and periodontal parameters.