OBJECTIVES: The aim of the study was to determine public expenditure on medicines for rare diseases from the public health sector in the Czech Republic (CZ). METHODS: We identified orphan medicinal products (OMPs) registered by the European Medicines Agency (EMA) until December 2013 in the public database of EMA. In the base-case scenario, medicinal products available in the CZ were considered OMPs only within the interval of marketing authorisation date and December 2013 or OMP designation withdrawal date or date of withdrawal of use. Reports on consumption and real expenditures of these OMPs came from all health insurance companies in the CZ. Exchange rate of 25.4 CZK = 1 EUR was used. RESULTS: Overall, 86 OMPs were authorised within the European Union (EU) between 2008 and 2013. Of these, 50 OMPs (58.0%) were covered from the Czech public health insurance at some point within this period. The number of registered OMPs increased from 54 in 2008 to 84 in 2013, while the number of covered OMPs doubled from 24 to 41, respectively. The annual public expenditure on OMPs rose simultaneously from 43 to 72 million EUR, while the total expenditure on drugs increased from 1.7 to 2.0 billion EUR. The OMP share of total pharmaceutical sales grew steadily from 2.5% in 2008, reaching 3.4% in 2011 and plateaued at 3.6% in 2013. Twenty-one oncological OMPs (51.2%) generated up to 72.6% of the overall orphan costs in 2013. CONCLUSIONS: Compared to other EU countries, the Czech public expenditure on OMPs of 3.6% of all drugs seems to be relatively high. The major part of OMP costs is in oncological diagnoses. One of the limitations is the exclusion of designated OMPs not authorised by EMA since these OMPs still might be present on the market and reimbursed. This aspect needs further investigation.