Junctions isolate the apical from the basal-lateral surfaces and are required for the polarization of epithelial cells. Genetics of junction formation in Drosophila has identified numerous transmembrane and scaffolding proteins that assemble in membrane-associated complexes. This review focuses on recent findings suggesting that junctions are autonomous organizing centers for the establishment and maintenance of apical-basal polarity in epithelial cells as well as other polarized processes such as the orientation of the division apparatus.