Mouse 3T3 feeder layer has been utilized for epidermal and corneal epithelial cell culture to promote tissue-like cell stratification. However, the molecular mechanism underlying epithelial-feeder layer interactions remains poorly understood. Here, the feeder layer activity of six different mouse cell lines was examined in terms of the colony-forming efficiency (CFE) of primary limbal epithelial cells, including corneal epithelial stem/progenitor cells. When epithelial cells and feeder layers were separated by culture inserts, the CFE was significantly lower than that of epithelial cells, which were cultured with feeder cells on the same dish surfaces, implying that direct contacts between these cells and/or pericellular extracellular matrix (ECM) deposition by feeder layers have an important role in feeder layer activity. With TaqMan polymerase chain reaction assay, the gene expression of 29 ECM molecules and 32 cadherin family genes was profiled in two highest and two lowest cell lines in the CFE for limbal and oral mucosal epithelial cells. A significant difference in the expression correlated with the CFE was observed in six ECM molecules and four kinds of cadherin family genes. In these results, type VI collagen was confirmed to be able to promote the colony formation of epithelial cells in vitro effectively.