The aim of this study was to better characterise the molecular events that occur in the cells of the dentine-pulp complex during dental injury and repair. A novel temperature-sensitive extirpation technique and employment of piezo-power microdissection enabled the expression levels of growth factors and their receptors, osteogenic, mineralisation and inflammatory markers to be analysed and related to specific cells/tissues of the dentine-pulp complex from rodent and mature human healthy and carious teeth. However, to enable the high-throughput characterisation of several thousand genes simultaneously Affymetrix U133A arrays were screened using RNA isolated from healthy and carious human pulp. Bioinformatic analysis of GeneChip data identified 445 genes greater than 2-fold differentially expressed, 360 more and 85 less abundant in carious pulp, ten of which were novel ESTs. GeneChip results were confirmed by q- and sq~RT-PCR for selected known genes Adrenomedullin, DMPl, plus the ten ESTs. Analysis of the rodent homologues of these genes in a multiple tissue cDNA panel indicated that 3 ESTs were specifically expressed in dental tissue. The present study has provided better characterisation of molecular events important in dental tissue inflammation and repair, which may provide a foundation for developing improved future diagnosis and treatment modalities to dental disease.