In conservation biology, there is a general consensus that protected areas (PAs) are one of the most effective tools for biodiversity protection. Worldwide, the area of PAs is continually increasing. But is the effectiveness of biodiversity protection improving with it? Since many PAs only exist as “paper parks” (i.e. they exist on maps and in legislation but offer little actual protection), the answer is uncertain. Moreover, it has long been known that, not only an increase in the extent of PAs, but also the efficiency of their management is fundamentally important for effective nature conservation. Therefore, there is a wide-ranging discussion about the actual effectiveness of PAs and factors that influence it. In the course of the EU pre-accession phase, a comprehensive field mapping of natural habitats took place in the Czech Republic in years 2001−2004. The mapping results were used to designate Special Areas of Conservation (SACs) as part of the Natura 2000 network. In this study, the aim was to evaluate the effectiveness of this newly created system of SACs for protection of biodiversity represented by the mapped natural habitats. The NCEI index (Nature Conservation Effectiveness Index) was applied, calculated as the total area of a particular habitat type in all SACs in the Czech Republic divided by the total area of that same natural habitat in the entire Czech Republic. Habitat protection in the Czech Republic is focused primarily on the smallest types of rare habitats, many of which are classified as critically endangered. The Czech national system of SACs provides protection to a total of 4,491.68 km2 of natural habitats. Based on these results, it can be concluded that the overall effectiveness of the SAC system in the Czech Republic, which is specifically aimed at protecting natural habitats, is low (NCEI = 0.36). Nevertheless, the critically endangered habitats receive maximum protection (NCEI = 1).