The security of embedded systems containing sensitive data has become a main concern. These widely deployed devices are subject to physcial attacks, requiring protections both in hardware and software. The race for higher productivity and shorter time to market in the deployment of secure systems pushes for automatic solutions. This thesis studies the integration of software countermeasures against fault attacks in development tools, with a special focus on the compiler. The goal is to enable the automatic application, at compilation time, of a wide range of countermeasures. We propose two protection schemes against these attacks which can be automatically deployed: one scheme dedicated to loop control flow and the second dedicated to the p...