In most eukaryotic cells microtubules undergo post-translational modifications such as acetylation of alpha-tubulin on lysine 40, a wide-spread modification restricted to a subset of microtubules that turns over slowly(1). This subset of stable microtubules accumulates in cell protrusions(2) and regulates cell polarization(3), migration and invasion(4-7). However, mechanisms restricting acetylation to these microtubules are unknown. Here we report that clathrin-coated pits (CCPs) control microtubule acetylation through a direct interaction of the alpha-tubulin acetyltransferase alpha TAT1 (refs 8, 9) with the clathrin adaptor AP2. We observe that about one-third of growing microtubule ends contact and pause at CCPs and that loss of CCPs decreases lysine 40 acetylation levels. We show that alpha TAT1 localizes to CCPs through a direct interaction with AP2 that is required for microtubule acetylation. In migrating cells, the polarized orientation of acetylated microtubules correlates with CCP accumulation at the leading edge(10), and interaction of alpha TAT1 with AP2 is required for directional migration. We conclude that microtubules contacting CCPs become acetylated by alpha TAT1. In migrating cells, this mechanism ensures the acetylation of microtubules oriented towards the leading edge, thus promoting directional cell locomotion and chemotaxis.