OBJECTIVES: Experience indicated that the quality of economic evaluations submitted in reimbursement dossiers and critical appraisals are heterogeneous. The objective of this study was to analyse the quality of submitted economic studies and related critical appraisal processes and to develop a policy-relevant, publicly available Slovak critical appraisal checklist for improving the quality of economic evaluation and budget impact analyses for reimbursement submission of dossiers concerning to drugs and medical devices. METHODS: We created a working group to review previously submitted economic evaluations and related critical appraisals in order to identify potential technical and methodological problems. The working group consisted of independent academic experts who scrutinized previous submissions and critical appraisals and developed a new checklist. Overall 50 economic evaluations submitted for reimbursement of drugs and medical devices in 2007-2009 were scrutinized. RESULTS: Evidence suggests that Slovak pharmaceutical expenditures do not result in the most cost-effective outcomes. Several potentially not cost-effective pharmaceuticals have been reimbursed in Slovakia. Economic evaluations of drugs and medical devices are mandatory but the quality of evaluations and critical appraisals are rather poor. Therefore in addition to the available Slovak health economic evaluation guidelines a detailed checklist for appraisal processes have to be prepared. Our analysis shows that the simplified questionnaire, which is currently used for the critical appraisal process within Slovakia should be replaced by a new Slovak critical appraisal checklist, which will be detailed enough to address the most common problems in the local economic evaluations and budget impact analyses for decision making process.     CONCLUSIONS: The transparent method of technology assessment can improve the consistency of reimbursement decisions making related to drugs and medical devices in Slovakia. The current checklist for critical appraisal is not sufficient enough and there is significant room for improvement in this field.