Background: A difference from the normal range in collagen profile and perivascular hyaline deposition in the dermis and gingiva has been demonstrated histopathologically in juvenile hyaline fibromatosis (JHF), which is an autosomal recessive disease. The aim of this study was to understand the mechanism of gingival overgrowth in JHF, and to observe differences in the expression of genes regulating extracellular matrix organization. Methods: Human gingival fibroblasts (GF) were obtained from individuals who have clinically healthy gingival tissue. JHF-GF were obtained from a patient who underwent a gingivectomy. Cultured fibroblast cells were examined visually using a phase contrast microscope. Total RNA from both cell types was isolated, and after biotin-deoxyuridine triphosphate (dUTP) labeling of cDNA, hybridization was performed with a pathway-specific gene expression profiling array membrane. Extracellular matrix (ECM) and adhesion molecule (AM) mRNA expressions in GF and JHF-GF were analyzed, and microarray data on genes modulating ECM remodeling were confirmed with reverse transcription-polymerase chain reaction (RT-PCR). Results: Cell morphology differences were observed between fibroblast types. Although type I collagen gene expression levels were almost the same, decreased type IV collagen expression was noted in JHF-GF versus GF. Decreased matrix metalloproteinase (MMP) and increased tissue inhibitor of matrix metalloproteinase (TIMP) transcripts were noted in JHF-GF versus GF. Increased fibronectin and decreased laminin mRNA expression were observed in JHF-GF when compared to GF. The present findings suggest that GF and JHF-GF differ not only morphologically but also in the expression level of ECM and AM genes involving connective tissue turnover and remodeling. Conclusions: Results from these analyses may be helpful to clarify the nature of overgrowth mechanisms, especially regarding enzymes and their inhibitors. This information is important in understanding the remodeling of ECM. The gingival overgrowth that is observed in JHF patients may be explained by a decreased level of MMPs and increased blockage of MMPs with TIMPs.