Intestine contributes to lipid homeostasis through the absorption of dietary lipids, which reach the apical pole of enterocytes as micelles. The present study aimed to identify the specific impact of these dietary lipids-containing micelles on gene expression in enterocytes. We analyzed, by micro-array, the modulation of gene expression in Caco-2/TC7 enterocytes in response to different lipid supply conditions that reproduced either the permanent presence of albumin-bound lipids at the basal pole of enterocytes or the physiological delivery, at the apical pole of lipid micelles, which differ in their composition during the inter-prandial (IPM) or the post-prandial (PPM) state. These different conditions led to distinct gene expression profiles. We observed that, contrary to lipids supplied at the basal pole, apical lipid micelles modulated a large number of genes. Moreover, when compared to the apical supply of IPM, PPM specifically impacted 46 genes from 3 major cell function categories: signal transduction, lipid metabolism and cell adhesion/architecture. Results from this first large-scale analysis underline the importance of the mode and polarity of lipid delivery on enterocyte gene expression. They demonstrate specific and coordinated transcriptional effects of dietary lipids-containing micelles that could impact the structure and polarization of enterocytes and their functions in nutrient transfer.