Toll-like receptor (TLR) signaling is thought to be one of the most important pathways initiating periodontitis onset. We have previously reported that the TLR signaling pathway is upregulated in periodontitis-affected gingival tissues by microarray pathway frequency analysis. The aim of the present study was to quantitatively analyze specific upregulated genes in the TLR signaling pathway, as compared to healthy controls. Healthy and periodontitis-affected gingival tissues were taken from distinct sites of 3 patients with severe chronic periodontitis. Total RNAs from 6 gingival tissue samples were used for microarray. Samples were taken from 14 chronic periodontitis patients and 14 healthy individuals for quantitative reverse transcription real-time polymerase chain reaction (qRT-PCR) analysis. Data-mining analyses, such as pathway analyses, were performed and significant biological pathways in periodontitis were identified. In addition, qRT-PCR analysis was performed for 5 genes—cluster of differentiation 14 (CD14), lymphocyte antigen 96 (MD-2), interleukin-1 beta (IL-1β), interleukin 8 (IL-8), and chemokine ligand 9 (CXCL-9), which are associated with TLR signaling, in order to confirm the results of pathway analysis. qRT-PCR verified that the transcripts for 5 genes in the TLR signaling pathway were significantly upregulated (MD-2 p = 0.0082, CD14 p = 0.0322, IL-1β p = 0.0126, IL-8 p = 0.0438, CXCL-9 p = 0.0325), which was consistent with pathway analyses. We confirmed upregulated MD-2 gene expression levels and associated TLR pathway gene expression, including CD14, IL-1β, IL-8 and CXCL-9, in periodontitis-affected gingival tissues, as compared with healthy controls.