OBJECTIVES: In the CZ, orphan drugs so-called highly innovative drugs first enter a temporary reimbursement period of three years. Having proven their cost-effectiveness they later become permanently reimbursed. The objective of the study was to determine how successfully orphan drugs enter the database of reimbursed drugs. METHODS: The EMA list of orphan drugs was compared to the Czech database of reimbursed drugs to the date of 1-Jul-2013. For each detected drug the date of entering the database was found. In drugs reimbursed after 2008, submissions of cost effectiveness analyses were recorded. Although CZ has no willingness to pay threshold, interpretation of cost effectiveness analyses results could improve the process of HTA of drugs.  RESULTS: To the date of 1-Apr-2013 the EMA has registered 65 orphan drugs. Out of these, 28 have been assigned a maximum and reimbursement price in the CZ. To this date, 27 drugs have not applied for reimbursement price. Starting from 2008, 30 drugs have applied: in 20 products the decision is legally effective, in 2 cases only hospital use has been approved, in 7 cases (3 appeals, 4 unfinished proceedings) the proceedings are still in process and in one case the application was withdrawn. In about a third of cases a cost effectiveness analysis was submitted and accepted by SUKL. The upper limit of the ICER of the submitted analyses exceeds by far the cost-effectiveness level recommended by the WHO. CONCLUSIONS: The results imply that in almost in all cases the submitted applications for maximum and reimbursement price are approved by SUKL. In some cases, however, the health insurance companies hinder reimbursement of drugs by filing an appeal. However, the assessment of cost effectiveness of drugs should be performed at an earlier level – during the administrative proceedings. This calls for necessary emphasis on health technology assessment