This book constitutes the refereed proceedings of the Third International Workshop on Fault Diagnosis and Tolerance in Cryptography, FDTC 2006, held in Yokohama, Japan in October 2006. The 12 revised papers of FDTC 2006 are presented together with nine papers from FDTC 2004 and FDTC 2005 that passed a second round of reviewing. They all provide a comprehensive introduction to the issues faced by designers of robust cryptographic devices.