We demonstrate the development of a new atmospheric pressure-atomic layer deposition(AP-ALD) system to coat the inner walls of capillary columns for gas chromatography (GC). Unlike traditional ALD, this reactor operates at near-atmospheric pressure and addresses the challenges of depositing thin films inside capillaries, which include long pump down times, deposition in high-aspect-ratio materials, and temperature control. We show ALD of alumina in 5 and 12 m capillaries (0.53 mm ID) via sequential half reactions of trimethylaluminum and water. Our system yields pinhole-free, uniform thin films. It includes small witness chambers for witness silicon shards before and after the capillary. An engineering flow/transport analysis of the device is provided. Our ALD alumina thin films are characterized by spectroscopic ellipsometry (SE), X-ray photoelectron spectroscopy, transmission electron microscopy (TEM), and energy-dispersive X-ray spectroscopy. Alumina film growth achieved is 1.4-1.5 Å/cycle, which is consistent with previously reported results. Film thickness measurements by SE on witness shards of silicon and by TEM at both ends of the capillary are in good agreement. A capillary column coated with alumina is used to separate different gases by GC, although the retention times of gases are essentially the same as with an untreated fused silica capillary. This successful deposition of ALD alumina in long capillaries opens the door for other possible ALD coatings, including hybrid organic-inorganic coatings, using the 450+ ALD precursors available today.