Abstract: An improved system is described for cooling high power waveguides by the use of cooling ducts extending along the waveguide, which minimizes hot spots at the flanges where waveguide sections are connected together. The cooling duct (24) extends along substantially the full length of the waveguide section, and each flange (18, 20) at the end of the section has a through hole (36) with an inner end connected to the duct and an opposite end that can be aligned with a flange hole in another waveguide section. Each flange (20) is formed with a drainage groove (60) in its face, between the through hole (36) and the waveguide conduit (16) to prevent leakage of cooling fluid into the waveguide. The ducts have narrowed sections (32, 34) immediately adjacent to the flanges to provide room for the installation of fasteners closely around the waveguide channel.