This paper discusses the link between accountability and internal auditing, particularly analyzing the extent to which the latter contributes to improve the former, in Higher Education Institutions (HEIs). This study applied a questionnaire to the management boards of a sample of HEIs, to empirical analyze the relationship between internal auditing and accountability. The main focus was on internal auditing carried out by the offices or departments in those institutions. The paper contributes to understand how management boards perceive internal auditing to foster transparency and accountability in HEIs, allowing to corroborate that auditing, and particularly internal auditing, favors the institutions’ accountability. In effect, it promotes the principles underlying accountability practices. The information provided in the scope of internal audits is acknowledged as contributing to improve management effectiveness and helping in decision-making. HEIs wanting to create an internal auditing office or to enhance the role of an existing one, should develop this office’s activities so that it becomes an instrument to support accountability and good governance of the organization. The sample consisted of Portuguese public HEIs, universities and polytechnics. Despite a certain international convergence regarding this type of public sector organizations, and regarding their purposes and governance, certain contextual specificities might limit the generalization of the findings for other jurisdictions.