Crossing single-walled carbon nanotubes can be joined by electron beam welding to form molecular junctions. Stable junctions of various geometries are created in situ in a transmission electron microscope. Electron beam exposure at high temperatures induces structural defects which promote the joining of tubes via cross-linking of dangling bonds. The observations are supported by molecular dynamics simulations which show that the creation of vacancies and interstitials induces the formation of junctions involving seven- or eight-membered carbon rings at the surface between the tubes.