OBJECTIVES: Since 2008 the Czech legislation requires health economic analysis (HEA) to be a part of all new drug reimbursement applications submitted to State Institute for Drug Control (SUKL): without any specific guidelines, however. In order to see the real-world impact of the legislation change, we investigated past (2008/2009) innovative molecules’ dossiers in terms of quality of their HEAs according to newly (2012) developed methodology of SUKL and also their impact on the respective decisions on coverage. METHODS: We selected all (22) applications for innovative drugs limited to specialized centers. We then briefly described the HEAs in terms of their perspective and type of analysis. The HEAs were further confronted with a ‘HEA checklist’ based on the new SUKL methodology to identify common drawbacks and faulty issues in past HEAs. Consequently the respective coverage decisions were investigated. RESULTS: Of the innovative molecules’ 22 dossiers investigated, only in 13 (59%) HEA was present. Two (15%) were cost-minimization studies, the rest were cost-effectiveness analyses, of which three (23%) were cost-utility. There was no apparent standardization in the analyses along with an obvious lack of transparency. Indeed, ‘proper description of input data and their sources’ was the point in the HEA checklist to be most often marked as ‘unsatisfactory’. Review of the consequent SUKL’s coverage decisions revealed that, irrespective of the HEA quality and even presence, all 22 (100%) applications were given a positive coverage decision. CONCLUSIONS: The present pilot study showed that in the first two years since introducing the obligation of health economic analyses be part of coverage applications, the system was largely ineffective. This finding stresses the necessity of introduction of a standardized methodology into the assessment and appraisal processes. Moreover, our study identified the key problematic areas to be specifically addressed by both the authors and assessors of future analyses.