To perform a‐proof‐of principle experiment of a SASE based Free Electron Laser a permanent magnet undulator has been installed in the TTF linac phase 1. The magnets used (NdFeB) are known to be sensitive to radiation damages if exposed to high energy electrons. Already beam losses in the order of 10−6of the nominal TTF beam current (64&mgr;A) are critical for the undulator and could have cause an irreversible damage of its magnets after a few months of operation. The protection of the undulator against radiation has been attacked twofold: first, a two stage spoiler‐absorber collimation system has been installed and second, a beam loss detection system of high sensitivity has been added to the machine protection system. The performance and the operational experience of the active and the passive protection system are discussed. © 2003 American Institute of Physics