Background and Aims: Achieving the desirable academic independence, requires the creation of appropriate structures and programs. This study has conducted with the aim of investigating the academic independence gap, from the Noshirvani and Medical Sciences University experts’ viewpoint.Methods: This study is descriptive-survey. The statistical population consisted of 50 experts of two Noshirvani and Medical Sciences University. In order to collect data, two researcher- made questionnaire (current and desirable situation of academic independence) were used. To analyze the data, Wilcoxon test was used by means of software Spss18.Results: There are gaps in all aspects of academic independence in both Universities. In Noshirvani University, the maximum to minimum gap is related to the staff, actual, organizational, financial independence, and academic freedom dimensions and in Babol Medical Sciences University, it includes organizational, staff, actual, financial independence, and academic freedom. Financial and organizational independence gap, and academic freedom in Medical Sciences University is rather than of Noshirvani University and staff and actual independence gap of the Noshirvani University is more than the Medical Sciences University.Conclusions: the presence of a gap between the present and desirable status of all aspects of academic independence in two universities, indicate the demand of academic independence. The tendency to acquire academic independence components in these universities and existing gap perception, represents the desire to growth and development. Planning and enforcement actions to reduce or eliminate existing gap are the key factors for achieving the desired academic independence and, consequently, the development in all fields.