After re-examination of this Letter, concerns with some of the reported data were raised. It was found that two confocal images were near-identical in panels of Figure 3 and two confocal images were re-used in panels of Figure 4, and that some gel images were inappropriately generated by cutting and pasting of non-adjacent bands. Therefore, we feel that the most responsible action is to retract the paper. We sincerely apologize for any adverse consequences that may have resulted from the paper’s publication. Recent evidence indicates a correlation between orientation of the plant cortical microtubule cytoskeleton and localization of polar cargoes(1). However, the molecules and mechanisms that create this correlation have remained unknown. Here we show that, in Arabidopsis thaliana, the microtubule orientation regulators CLASP(2,3) and MAP65 (refs 3, 4) control the abundance of polarity regulator PINOID kinase(5,6) at the plasma membrane. By localized upregulation of clathrin-dependent endocytosis(7) at cortical microtubule- and clathrin-rich domains orthogonal to the axis of polarity, PINOID accelerates the removal of auxin transporter PIN proteins(8-10) from those sites. This mechanism links directional microtubule organization to the polar localization of auxin transporter PIN proteins, and clarifies how microtubule-enriched cell sides are kept distinct from polar delivery domains. Our results identify the molecular machinery that connects microtubule organization to the regulation of the axis of PIN polarization.