OBJECTIVES: The Slovak guidelines for economic evaluation, although appearing to be generic, have been written focusing on pharmaceuticals. The objective of this study was to analyse the quality of submitted economic studies and related critical appraisals process and to develop a policy-relevant, publicly available Slovak critical appraisal checklist for improving the quality of economic evaluation for reimbursement submission of dossiers concerning to 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 two independent academic experts who scrutinized previous submissions and critical appraisals concerning to medical devices between 2007-2010. RESULTS: Evidence suggests that the methods of economic evaluation can be equally applied to drugs and devices in general. However, there are several specific methodological issues that require more attention if reliable and informative evaluations of devices are to be conducted. These issues are underestimated within the Slovak Republic. It is well known that expenditures for medical devices do not result in the most cost-effective outcomes. Economic evaluations of medical devices are mandatory but the quality of evaluations and critical appraisals are poor. 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 specific problems in the local economic evaluations process. CONCLUSIONS: The transparent method of technology assessment can improve the consistency of reimbursement decisions making related to medical devices in Slovakia. Therefore in addition to the available Slovak health economic evaluation guidelines a detailed checklist for appraisal processes specific for medical devices have to be prepared. The economic evaluation of devices raises additional challenges and the current Slovak guidelines overlook several issues.