Background: Clinical and radiographic measures are gold standards for diagnosing periodontitis but offer little information regarding the pathogenesis of the disease. We hypothesized that a comparison of gene expression signatures between healthy and diseased gingival tissues would provide novel insights in the pathobiology of periodontitis and would inform the design of future studies.Methods: Ninety systemically healthy non‐smokers with moderate to advanced periodontitis (63 with chronic periodontitis and 27 with aggressive periodontitis) each contributed at least two diseased interproximal papillae (with bleeding on probing [BOP], probing depth [PD] ≥4 mm, and attachment loss [AL] ≥3 mm) and a healthy papilla, if available (no BOP, PD ≤4 mm, and AL ≤2 mm). RNA was extracted, amplified, reverse‐transcribed, labeled, and hybridized with whole genome microarrays. Differential expression was assayed in 247 individual tissue samples (183 from diseased sites and 64 from healthy sites) using a standard mixed‐effects linear model approach, with patient effects considered random with a normal distribution and gingival tissue status considered a two‐level fixed effect. Gene ontology analysis classified the expression patterns into biologically relevant categories.Results: Transcriptome analysis revealed that 12,744 probe sets were differentially expressed after adjusting for multiple comparisons (P <9.15 × 10−7). Of those, 5,295 were upregulated and 7,449 were downregulated in disease compared to health. Gene ontology analysis identified 61 differentially expressed groups (adjusted P <0.05), including apoptosis, antimicrobial humoral response, antigen presentation, regulation of metabolic processes, signal transduction, and angiogenesis.Conclusion: Gingival tissue transcriptomes provide a valuable scientific tool for further hypothesis‐driven studies of the pathobiology of periodontitis.