This study used microarray technology to analyze gene expression in gingival tissue samples from refractory periodontitis patients and periodontally well-maintained patients. The results showed 68 upregulated genes and 6 downregulated genes in refractory periodontitis patients. Real-time PCR analysis of selected genes validated the microarray results, confirming differential expression of genes related to the host immune response and tissue destruction in refractory periodontitis. The gene expression profile provides insights into the dysregulated biological pathways that may contribute to treatment failure in refractory periodontitis.