Research is a systematic, controlled empirical and critical study for the discovery of the relationships between phenomena. It also presents various hypotheses, and seeks to achieve a specific purpose and action. It emphasizes the welfare and prosperity of everyone. Undoubtedly, researches should meet the country's scientific and technological needs and generate wealth. But the events in higher education, such as unaccountable scientific works, the decline of research efficiency, etc. have called these assumptions into question. For what reasons our country has not been able to take effective steps in the field of research and is unable in meeting the needs of society despite its potential in this subject and its researchers? The purpose of this study was to identify and explain the factors affecting the occurrence of research biases in the Iranian higher education system using a qualitative content analysis approach. Data were collected through deep and semi - structured interviews with 22 of top researchers, experts and research policy makers in 2018-2019 by a purposeful sampling method. Findings showed that existing structural problems, university not focusing on mission, weaknesses of university, industry and community relationship, article orientation, weakness of evaluation system, downfall of academic community standards, incorrect system of student acceptance and faculty recruitment, as well as the weakness of the legal structure are some of the main causes of research malfunctions in Iranian universities and higher education institutions.