Numerical classification of 2653 geographically stratified relevés of weed vegetation from the Czech and Slovak Republics was performed with cluster analysis. Diagnostic species were determined for each of the seven main clusters using statistical measures of fidelity. The classification reflected clear distinctions between lowland (mostly calcicole) and highland (mostly calcifuge) sites, spring and summer phenological stages, and cereals and root crops. The results of the cluster analysis were compared with traditional phytosociological units. Two clusters corresponded to calcifuge weed vegetation of the Scleranthion annui alliance; one cluster represented the vegetation of root crops on moist soils of the Oxalidion europaeae alliance; one cluster contained thermophilous weed vegetation of the Caucalidion lappulae alliance; two clusters included weed vegetation of root crops and of stubble fields, which can be assigned to the Caucalidion, Panico-Setarion, Veronico-Euphorbion and Eragrostion alliances; one cluster included vernal weed vegetation in little disturbed habitats of the Caucalidion lappulae and Scleranthion annui alliances. Our analysis did not support the concept of the Sherardion and Veronico-Taraxacion alliances, which were included in earlier overviews of the vegetation units of the Czech Republic and Slovakia.