Gene chip was a high-throughput, rapid, parallel nucleic acid sequence detection and quantitative analysis technology. It has been widely used in molecular biology in recent years. Study on dental pulp genomics will help to understand the physiological and pathological mechanisms of pulp, thus contributing to the clinical application in prevention, diagnosis and treatment. In this review, we briefly described the gene chip technology and its applications in dental pulp stem cells, aged dental pulp and dental caries.