In this paper some directions of innovation activity in the system of engineering education are analyzed. The scheme of innovative engineering education is suggested which takes into account different technologies and directions of specialist training. Unless additional measures for protection of interests of the national education are taken, Russia's accession to the WTO can have more negative than positive effects for the Russian higher school. The main task of the Russian higher school is to modify the Russian legislation in a comprehensive way for the purpose of creation of favorable conditions for Russian higher education institutions and development of the Russian education.