Flora Europaea represents a basic source of information on the flora of European countries. Since it contains detailed treatment of naturalized species, it is used as a data source in comparative analyses of alien floras. By using the Czech Republic as a model country, for which solid information on alien species is available, the present paper assesses the reliability of data on alien species contained in Flora Europaea and critically evaluates their potential for utilization in comparative analyses. Of the 332 naturalized species reported in Flora Europaea for the territory of the former Czechoslovakia, some species are relevant only to the territory of Slovakia and some are planted species and never reported escaping from cultivation in the Czech Republic. By excluding these species, there are 312 species relevant to the Czech Republic and supposedly naturalized in this country. Among these, there are 7 species now considered native and 15 are erroneous records of plants which never occurred in the country. In total, there are 290 species (92.9% of the 312 reported) correctly identified by Flora Europaea as aliens to the Czech flora. Of these species, considered by Flora Europaea as naturalized, only 118 in fact do have this status. The remaining 172 species are casuals. After excluding I I species casual in the Czech Republic but naturalized in Slovakia, there are 161 species, i.e. 55.5% of the 290 reported, with incorrect status given in Flora Europaea. Another 111 naturalized species (48.5% of those currently known) are missing from the account on alien species in Flora Europaea. It is argued that while Flora Europaea can be, with careful interpretation, used for identifying robust patterns based on species numbers, it cannot be used for in-depth analyses of invasion pattern across Europe, namely for studies on the naturalization success in different parts of the continent, since the data it contains are highly unreliable in terms of evaluating species invasion status. These results indicate that there is an urgent need to include the issue of alien species in integrated European projects.