This study was an attempt to investigate obstacles ahead of the establishment of internal auditing unit in Iranian State Universities. The study was conducted through engaging and investigating 193 sample population of auditors and expert’s opinions in academic settings and those professionals in non-academic settings. To identify the Obstacles, both statistical tests including one sample T test and factor analysis were run. The findings revealed that the obstacles ahead of establishment of internal auditing units were classified in 3 main groups including: 1. Legal, organizational and cultural obstacles, 2. Lack of knowledge, training and appropriate coordination, 3. Obstacles ahead of Internal Auditing personnel. Cultural, legal and organizational obstacles including restrictions related to the culture and rules governing the social and organizational context. Moreover, lack of knowledge, training and appropriate coordination indicated limitation of educational aspects affected by internal departments of an organization and professional institutions of community. In addition, the obstacles a head of personnel including shortage of specialists in auditing system of academic settings as well as unemployment of independent and experienced auditors in auditing units. The findings of this study are among determining factors of evolutionary planning of internal auditing units in public sectors and it may contribute to further developments and success.