Ministry of Health has set a Health Minimum Service Standards (HMSS) for District/City by Minister of Health Decree No. 741/Menkes/Per/VII/2008, which consist of 18 indicators. After three years of implementation, an analysis of the HMSS implementation has conducted. Using a cross-sectional study design, site selection is done purposively to represent Eastern, Central, and Western part of Indonesia. There were nine districts/cities of 9 provinces selected. The analysis showed that problems in the implementation of HMSS are: some indicators do not meet the SMART criteria, inconsistency between the title of indicators, operational definitions and formulas, wide gap in the coverage both within the district at different times and among districts/cities. Differences also occur at the operational level, including dissemination of HMSS, advocacy, monitoring and evaluation. It is recommended that the Ministry of Health should provide sufficient training, proper socialization of HMSS, set up a special unit to monitor and facilitate the implementation of HMSS. The existing MSS should be revised, no longer focusing on the achievement of the program but rather based on a form of health care provided. In addition, revision is necessary to gain consistency between definitions, operational definitions and formulas of HMSS indicators.