BACKGROUND: The application of Health Technology Assessment (HTA) and Pharmacoeconomics (PE) into real health policies in  selected European countries (Austria, Bulgaria, Croatia, Czech Republic, Germany, Hungary, Latvia, Poland, Romania, Serbia, Slovakia, Slovenia, UK) was analyzed based on the outputs from the conference „Optimalization of Methods of PE and HTA: Importance for National Health Policy and Cross-Border Cooperation” (Slovakia,10/2012). OBJECTIVES: The objective of the paper was to compare the systems and to find the most transparent one based on the pre-defined criteria. METHODS: The primary method used for the analysis was structured evaluation of the outputs from the conference. The other relevant information resulted from the systematic review of PUBMED, EMBASE and CENTRAL in years 2011-2012 extended to official websites of public health institutions and officially published data with the objective to select all papers on HTA/Pharmacoeconomics related to selected European countries. We evaluated 9 characteristics relevant for the decision-making process: legislative background, implementation, binding force, institutionalization, qualified personal resources availability, existed methodology/guidelines, clarity of the process, patient involvement in the process, and respecting the deadline of 180 days for issuing a decision. RESULTS: Resulting from the analysis, of selected countries, the United Kingdom was shown to have the most transparent system. Germany and Austria ranked second. Hungary and Poland ranked third, followed by Slovakia. The least transparent system was found in Bulgaria and Romania. CONCLUSIONS: One of the criteria was qualified personal resources availability that immediately discriminate systems in smaller central and eastern European countries. This should result in developing tailored approaches rather than copying technocratic “western” systems. The system prepared in Romania based on multiple criteria decision analysis principle could be regarded as a positive example.