We describe the fabrication and measurement of microwave coplanar waveguide resonators with internal quality factors above 10 7 at high microwave powers and over 10 6 at low powers, with the best low power results approaching 2 × 10 6 , corresponding to ∼ 1 photon in the resonator. These quality factors are achieved by controllably producing very smooth and clean interfaces between the resonators' aluminum metallization and the underlying single crystal sapphire substrate. Additionally, we describe a method for analyzing the resonator microwave response, with which we can directly determine the internal quality factor and frequency of a resonator embedded in an imperfect measurement circuit.High quality factor microwave resonators provide critical elements for superconducting electromagnetic radiation detectors 1 , quantum memories 2,3 , and quantum computer architectures 4 . Good performance and stability can be achieved for such applications using aluminum resonators patterned on sapphire substrates. Aluminum is a favored material due to its robust oxide and reasonable transition temperature, and sapphire provides an excellent substrate due to its very low microwave loss tangent 5 δ ∼ 10 −8 and its chemical inertness. However, the quality factors measured in such resonators is lower than expected; recent simulations 6 and experiments 7 suggest that the unexplained loss arises mostly from imperfections at the metal-substrate interface. Using an experimental apparatus with minimal stray magnetic fields and infrared light at the sample 8 , here we show that careful substrate preparation and cleaning yields aluminumon-sapphire resonators with significantly higher internal quality factors Q i . We also introduce a new method for evaluating the resonator microwave response.The aluminum for the resonators was deposited on cplane sapphire substrates in one of three deposition systems: A high vacuum DC sputter system (base pressure P base = 6 × 10 −8 Torr), a high vacuum electron-beam evaporator (P base = 5 × 10 −8 Torr) or an ultra-high vacuum (UHV) molecular beam epitaxy (MBE) system (P base = 6 × 10 −10 Torr) with electron-beam deposition. The sapphire substrates were first sonicated in a bath of acetone then isopropanol followed by a deionized water rinse. For the sputter-deposited and e-beam evaporated samples, we further cleaned the substrates prior to Al de-