Embedded systems are increasingly present in our daily lives (e.g. credit cards, smartphones and biometric passports). Given the sensitivity of the data they handle, the safety of these systems has become a major concern for industry and state organizations. It is established that a fault injection in an embedded system can compromise the security of the data it contains, for example obtaining a secret key or bypassing an authentication mechanism. The goal of this thesis is the automatic generation of software protections against fault injection attacks on embedded systems. The source and binary approaches consist in inserting the protections respectively in the source and binary code of the application; this thesis explores the use of a co...