Periodontitis is an inflammatory condition affecting periodontal tissues, such as the gingiva and alveolar bone, surrounding the teeth. However, previous research has focused on analyzing a single sample type, such as tissue, blood, or gingival crevicular fluid (GCF), which may limit the comprehensive understanding of the complex pathology of periodontitis. We conducted a proteomic analysis using liquid chromatography-mass spectrometry (LC-MS) on the periodontal tissues and GCF from patients with periodontitis. This analysis distinguished distinct proteomic signatures between the two sample types, with 3,803 proteins being identified in periodontal tissue and 910 proteins in GCF, underscoring the significant variances pertinent to periodontal health. Proteins such as S100A12, MPO, APOA1, CTSG, and PSMA1 were markedly upregulated in GCF, suggesting their potential as key markers of neutrophil activity and systemic inflammation. These findings provide profound insights into both the local and systemic pathophysiological processes underlying periodontitis, emphasizing the utility of GCF as a non-invasive medium for reflecting comprehensive disease states.