Undoubtedly, internal auditing has an effective situation on the corporate governance structure. Internal audit by timely identification of weaknesses in internal controls has a significant role in reducing fraud, manipulating of information, enhancing financial reporting and increasing the efficiency and effectiveness of the company. After the approval of the internal controls and the internal auditing charter in 1391(Iranian calendar) by the security exchange organization, the internal audit challenges and pathology are important. Many experts and managers in this area believe that many challenges, especially in the early years, has threatened internal auditing and has prevented its effectiveness. The present research, which is one of the survey research, conducted an interview, review of previous studies, produced, and tested a questionnaire using actual internal audit information. The society and the statistical sample included the directors and heads of internal audit, financial experts and members of the audit committees of the companies listed in the Tehran stock exchange and OTC of Iran. The number of respondents to the audit committee questionnaires has been sent 88 times three times. The weakness oversight of the security exchange organization, the lack of internal auditors' salaries and benefits, and finally, the not giving bonus are challenges of internal auditors. Additionally, internal auditors training, accreditation testing, lack of co-responsibility in several companies, revision of the internal audit charter, rewarding, ongoing meetings with independent auditors, and follow up of weaknesses in internal controls by the annual general meeting include are ways to improve the performance of internal audit.