Background: Public managers are always looking to achieve clear and accurate information about the financial performance of the organization to have better accountability in this area in addition to efficient management and improvement of indices.

  Objective: The aim of this study was t o evaluate the effect of implementing the accrual-based financial system on transparency and accountability.

  Methods: This survey was conducted in Qazvin University of Medical Sciences, 2013. The study population consisted of 70 financial managers, auditors of Supreme Audit Court, heads of accounting units, financial and budget staff , middle and high rank managers, auditors of Board of Trustees of Qazvin University of Medical Sciences that were selected by random sampling method. The measurement tool was a two-part questionnaire consisted of 15 questions for financial transparency, 11 questions for financial accountability in three dimensions and 6 questions for operational accountability in three dimensions. Data were analyzed using one-sample T-test.

  Findings: There were statistically significant relationship between the implementation of the accrual-based financial system and the followings: increased financial transparency and the possibility for assessment of the approved budget control , the application of the financial regulations, the financial reporting to increase financial accountability and the possibility for assessment of efficiency and economic profit to increase operational accountability . The association of the accrual-based financial system and the possibility for assessment of effectiveness to increase operational accountability was not statistically significant.

  Conclusion: With regards to the results, the implementation of the accrual-based financial system led to increased financial transparency and financial and operational accountability in Qazvin University of Medical Sciences.