The human intestinal Caco‐2 cell line has been extensively used as a model of the intestinal barrier. However, it is widely reported in literature that culture‐related conditions, as well as the different Caco‐2 cell lines utilized in different laboratories, often lead to problems of reproducibility making difficult to compare results. We developed a new cell‐maintenance protocol in which Caco‐2 cells were subcultured at 50% of confluence instead of 80% of confluence, as usually suggested. Using this new protocol, Caco‐2 cells retained a higher proliferation potential resulting in a cell population, which, on reaching confluence, was able to differentiate almost synchronously, forming a more homogeneous and polarized cell monolayer, as compared to that obtained using a high cell growing density. This comparison has been done by analyzing the gene expression and the structural characteristics of the 21‐days differentiated monolayers by microarrays hybridization and by confocal microscopy. We then investigated if these differences could also modify the effects of toxicants on 21‐days‐differentiated cells. We analyzed the 2 h‐acute toxicity of CuCl2 in terms of actin depolymerization and metallothionein 2A (MT2A) and heat shock protein 70 (HSPA1A) genes induction. Copper treatment resulted in different levels of actin depolymerization and gene expression induction in relationship with culture protocol, the low‐density growing cells showing a more homogeneous and stronger response. Our results suggest that cell growing density could influence a number of morphological and physiological properties of differentiated Caco‐2 cells and these effects must be taken in account when these cells are used as intestinal model. J. Cell. Physiol. 226: 1531–1543, 2011. © 2010 Wiley‐Liss, Inc.