This paper discusses structural and ideological challenges to mother tongue-based multilingual education (MTB-MLE) which has in recent years been gaining ground in many educational contexts around the world. The paper argues, however, that MTB-MLE is set against these challenges - referred to here as inequalities of multilingualism - which prevent MTB-MLE from being implemented successfully. The first section provides a brief background of significant phenomena which have led to the emergence of MTB-MLE as a viable form of education around the world. The second section describes some features of inequalities of multilingualism by situating the paper within sociolinguistic and sociopolitical contexts in Asia, especially Southeast Asia, to be followed further in the third section with a more targeted discussion of such inequalities using a recent case of linguistic discrimination in the Philippines as an example. The paper highlights the continuing vulnerabilities of mother tongues in education even if official discourse and policy seem to work for them.