Eleven proteins encoded by influenza A viruses play different roles in host receptor recognition, cross-species transmission, virus replication, pathogenicity, and induction of host immune responses. Understanding of the pathogenic mechanism of mutations in influenza A virus-encoded proteins could offer new targets for the development of universal vaccines and effective drugs against highly pathogenic influenza viruses. Based mainly on the current literature, this article is intended to provide a comprehensive analysis of progresses in amino acid variations in influenza A virus-encoded proteins and their relationships to pathogenicity as well as cross-species transmissibility.