Epidermal growth factor peptide binding was analyzed on primary cultures of colonic cells and along crypts by fluorescent laser-scanning confocal microscopy, using a three-dimensional image analysis software (Quant3D, Linux/Unix). Structural, proliferative units from primary cultures grown in rotating bioreactor for 41 d were arranged according to a tubular symmetry or on a parallelepiped sheet. Mean width, height, and depth of 23 tissue-like masses (± standard error) were 125 μm (±16), 152 μm (±23), and 29 μm (±3), respectively. Mean density of nuclei in tissue-like masses, expressed as the number of nuclei per cubic millimeter (± standard error of the mean), was 1.8 × 10⁵ (±0.7 × 10⁵) nuclei per cubic millimeter, which corresponded to a density that was five to six times lower than that estimated for the colonic crypt isolated by chelation. Spots of high epidermal growth factor (EGF) peptide binding that corresponded to microlesions in crypt monolayers or to active colonization of microcarriers by epithelial and stromal cells in tissue-like masses were observed. The relative intensities of EGF peptide binding that were obtained below cell position 8 on crypts were very homogeneous and were representative of the profile obtained with crypts isolated from adult rats adapted to a normal diet and used to develop primary cultures of colonocytes in our laboratory. A microscopic multidimensional analytic system to record the expression profiles of biomarkers along intestinal tissues should enhance the use of primary cultures of colonocytes for in vitro testing of new food products.