OBJECTIVES: The aim of the present analysis was to identify what was the influence of prices and the corresponding low cost-effectiveness estimates of the appraised orphan drugs on AHTAPol recommendations. The main task of AHTAPol, established  in  2005, is to assess and appraise all medical technologies and services claiming public money founding. Pharmacoeconomic evaluations of new therapies are required for all reimbursement  decisions and orphan drug manufacturers cannot be exempted from providing a full pharmacoeconomic or HTA  reports. Recommendations issued by AHTAPol have been based on Manufacturer`s submission, additional officially published data, experts opinions and Polish public payer (National Health Fund) evaluation. METHODS: All recommendations issued by the AHTAPol until the end of 2010 were reviewed and analyzed from the official Web site of AHTAPol.  The orphan drugs recommendations were identified and categorized into types of recommendations (positive or negative) and reasoned. RESULTS: Among 286 AHTAPol decisions studied, 26 (9%) applied to orphan drugs. AHTAPol gave positive recommendations for reimbursement to 19 of 26 of orphan drug submissions (73%). 7 (27%)  were not approved and received negative recommendations. Only in one case cost-effectiveness estimates and the corresponding high prices were  emphasized as a main reason of negative recommendations. In 1 case the reason was connected with drug safety issues, while in 5 cases with  insufficient evidence of efficacy. CONCLUSIONS: The cost-effectiveness issues of the appraised orphan drugs were not important argument in negative recommendations of the AHTAPol. In fact the insufficient evidence of clinical efficacy were the most important and therefore prevailing argument for issuing  negative opinions of AHTAPol recommendations.