Considering the McEliece cryptosystem using quasi-cylcic MDPC (Moderate Density Parity Check matrix) codes allows us to build a post-quantum encryption scheme with nice features. Namely, it has reasonable key sizes and both encryption and decryption are performed using binary operations. Thus, this scheme seems to be a good candidate for embedded and lightweight implementations. In this case, any information obtained through side channels can lead to an attack. In the McEliece cryptosystem, the decryption process essentially consists in decoding. As we consider the use of an iterative and probabilistic algorithm, the number of iterations needed to decode depends on the instance considered and some of it may fail to be decoded. These behaviors are not suitable because they may be used to extract information about the secrets. One countermeasure could be to bound the number of encryptions using the same key. Another solution could be to employ a constant time decoder with a negligible decoding failure probability, that is to say which is about the expected security level of the cryptosystem. The main goal of this thesis is to present new methods to analyse decoder behavior in a cryptographic context.Second, we explain why a McEliece encryption scheme based on polar code does not ensure the expected level of security. To do so, we apply new techniques to resolve the code equivalence problem. This allows us to highlight several common properties shared by Reed-Muller codes and polar codes. We introduce a new family of codes, named decreasing monomial codes, containing both Reed-Muller and polar codes. These results are also of independent interest for coding theory.