Objective: To detect and analyze the differential expression profile of long non-coding RNA (lncRNA) in aggressive periodontitis (AgP) and healthy gingival tissues, in order to explore the role of lncRNA in AgP. Methods: After the informed consents were obtained, gingival tissues from AgP patients (n=40) and healthy volunteers (n=40) were collected in Department of Periodontology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (from Mar. 2012 to Aug. 2012) and Department of Periodontology, Hospital of Stomatology, Tianjin Medical University (from Oct. 2016 to Apr. 2017). The differential expression of lncRNA of tissues from AgP patients (n=20) and healthy volunteers (n=20) were examined via microarray assay. Bioinformatics was applied to analyze the expression data of lncRNA and correlative mRNA. Two lncRNAs (lncRNA-TNFRSF13C and lncRNA-API5) were chosen to verify the microarray results by using real time quantitative polymerase chain reaction (PCR) in the other gingival tissues. Results: Compared with the result of healthy gingival tissues, totally 8 632 lncRNAs were differentially expressed in tissues from AgP patients. From these data, 1 986 lncRNAs were significantly upregulated while 6 646 lncRNAs were downregulated, amongst which 48 lncRNAs were upregulated (>10 times) (P<0.05), 14 lncRNAs were downregulated (>10 times) (P<0.05). Furthermore, totally 5 519 correlative mRNAs were differentially expressed, amongst which 1 676 mRNAs were upregulated (≥2 times, P<0.05) and 3 843 mRNAs were downregulated≤0.5 (P<0.05). The selected lncRNA-TNFRSF13C and lncRNA-API5 were up-regulated in AgP (P<0.05), which confirmed the results of microarray. From bioinformatics, differential expression lncRNAs were in association with many signal pathways including toll-like receptor signaling pathway, cell cycle and apoptosis pathway, and tumor necrosis factor receptor superfamily pathway. Conclusions LncRNA may be involved in the pathogenesis of AgP through various pathways, which need to be further explored.