Background: Pentraxin 3 (PTX3) is associated with periodontal tissue inflammation, a condition that precedes alveolar bone resorption. It is also elevated in obese tissues and is a useful biomarker of proinflammatory status. Serum amyloid A (SAA) is a proinflammatory and lipolytic adipokine. Adipocytes strongly express SAA, which suggests that it may have a significant role in the production of free fatty acids and local and systemic inflammation. Materials and Methods: We statistically analyzed the gingival crevicular fluid (GCF) values of PTX3 and SAA in patients with periodontal disease, who were diagnosed with obesity, and compared them with the values of inflammatory markers from patients diagnosed with one of the diseases and with healthy patients. Results: The patients with obesity and periodontitis had significantly higher levels of PTX3 and SAA than the patients diagnosed with either obesity or periodontitis. Conclusions: These two markers are involved in the association between the two pathologies, as evidenced by the correlations between these levels and some clinical parameters.