Here we present the microwave characterization of microstrip resonators made from aluminum and niobium inside a 3D microwave waveguide. In the low temperature, low power limit internal quality factors of up to one million were reached. We found a good agreement to models predicting conductive losses and losses to two level systems for increasing temperature. The setup presented here is appealing for testing materials and structures, as it is free of wire bonds and offers a well controlled microwave environment. In combination with transmon qubits, these resonators serve as a building block for a novel circuit QED architecture inside a rectangular waveguide.Microwave resonators are an important building block for circuit QED systems where they are e.g. used for qubit readout 1,2 , to mediate coupling 3 and for parametric amplifiers 4 . All of these applications require low intrinsic losses at low temperatures (k B T hf r ) and at single photon drive strength. In this low energy regime, the intrinsic quality factor, which quantifies internal losses, is often limited by dissipation due to two level systems (TLS) 5,6 . These defects exist mainly in metal-air, metalsubstrate and substrate-air interfaces as well as in bulk dielectrics 6-9 . Two common approaches exist, to improve the intrinsic quality factor of resonators. Either one reduces the sensitivity to these loss mechanisms by reducing the participation ratio 6,10,11 or tries to improve the interfaces by a sophisticated fabrication process 12,13 . Reducing the participation ratio requires to reduce the electric field strength. This is typically done by increasing the size of the resonator 8 or even implementing the resonator using three dimensional structures 10 .Our approach, a microstrip resonator (MSR) in a rectangular waveguide (Fig. 1), combines the advantages of three dimensional structures with a compact, planar design 2,14 . The sensitivity to interfaces is reduced, since the majority of the field is spread out over the waveguide, effectively reducing the participation ratio 11 . Another advantage is, that the waveguide represents a clean and well controlled microwave environment 15 without lossyseams 16 close to the MSR. As the MSR is capacitively coupled to the waveguide, no wirebonds 17 or airbridges 18 are required, which can lead to dissipation or crosstalk.The U-shaped MSR ( Fig.
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