The apical and basal faces of an epithelium are different: each contains a different set of molecules that reflect the polarized organization of the individual epithelial cells: each has a top and a bottom, with different properties and functions. This polarity is crucial for epithelial function.

For example, the simple columnar epithelium that lines the small intestine of a mammal. It mainly consists of two intermingled cell types: absorptive cells, which take up nutrients, and goblet cells (so called because of their shape), which secrete the mucus that protects and lubricates the gut lining. Both cell types are polarized.

The absorptive cells import food molecules from the gut lumen through their apical surface and export these molecules from their basal surface into the underlying tissues. To do this, absorptive cells require different sets of membrane transport proteins in their apical and basal plasma membranes. The goblet cells also have to be polarized, but in a different way: they have to synthesize mucus and then discharge it from their apical end only; their Golgi apparatus, secretory vesicles, and cytoskeleton are all polarized so as to bring this about.

For both types of epithelial cells, polarity depends on the junctions that the cells form with one another and with the basal lamina. These cell junctions in turn control the arrangement of an elaborate system of membrane-associated intracellular proteins that create the polarized organization of the cytoplasm.