This study aims to analyze the influence of human resources quality, accountability, transparency, and internal control on performance of value for money based budgeting (Empirical Study at The Puskesmas in Regional of Yogyakarta City). The object of this study is Puskesmas in Regional of Yogyakarta City. In this study use a sample of 64 respondents, that selected by purposive sampling. The data used are primary data, collected by using questionnaires. The analysis that used in this study are multiple linear regression with SPSS 15.0. The results of this study indicate that accountability and internal control have a positive significant effect on performance of value for money based budgeting. However, human resources quality and transparency have no effect on performance of value for money based budgeting.