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Interdisciplinary activities are in vogue and are used in institutional fields of “knowledge” and organizational gatherings form “education” and are creditable as a new method for knowledge production and educational policymaking. Despite sporadic resistance, “interdisciplinary activities” is not a focus of attention for institutions producing and promoting knowledge as well as organizational and social entities concerned with education. However, they are practically facing complex obstacles, serious challenges and criticism. This descriptive – analytical paper which emphasizes on interdisciplinary higher education, maintains that the most important obstacles and challenges faced by interdisciplinary activities in the past three decades can be divided into “organizational”, “professtional”, and “cultural” obstacles, In conclusion, special obstacles and challenges to interdisciplinary programs in humanities have been explained.