Project monitoring and evaluation is the most important part of the project life cycle. The purpose of this study is assessing the M&E practices of Integrated Service in Health Development Organization (ISHDO) regarding to skilled staff, budget allocation and management participation and their relationship with effectiveness of M&E. A descriptive research was used and both primary and secondary data were collected. A total of 45 respondents were targeted by the study and a questionnaire was used as a data collection tool. SPSS was used to analyze the data that are collected using questionnaire. In order to determine the relationship between the variables, Pearson correlation and regression analysis was conducted. Based on the results of the study, the variables; skilled staff, budget allocation and management participation has got a positive relationship in ISHDO. Hypothesis test was conducted by checking the significant value of the independent variables and from those variables skilled staff was rejected and the others were supported. Also the study tries to assess how the three factors are being practiced in the organization. The finding of this research shows that even if the three factors have a significance effect on the effectiveness of M&E systems, but they are poorly practiced and there is a gap regarding to their implementation. So the study recommends that frequent formal trainings, timely planning and submission of budget request and also an active managementsâ€™ participation are recommended in order to have an effective M&E.