The spatial distribution of cytotypes can provide valuable insights into the evolution of polyploid complexes. Previously, only tetraploid Allium oleraceum was reported from Slovakia. Analysing 863 individuals from 93 populations from Slovakia revealed an extensive variation in the DNA ploidy levels of Allium oleraceum (3x, 4x, 5x and 6x). Of the main cytotypes, the penta- and tetraploids had strongly overlapping distributions, although the pentaploids exhibited a tendency to occur more frequently in the southern and the tetraploids had a tendency to occur in the northern regions of Slovakia. A triploid cytotype was found in one population in the southern part of Slovakia, which is the third locality worldwide for this cytotype. The hexaploid cytotype was rare and sparsely occurred in western and southern Slovakia. Sixteen per cent of the populations sampled consisted of more than one ploidy level; the most common was a combination of penta- and tetraploids. The cytotypes differed with respect to altitude; the tetraploids were found significantly more frequently at higher altitudes than the penta- and hexaploids. When compared with reanalysed altitudinal distribution data from the Czech Republic divided into two geographic areas (Carpathian and Herzynian) the pattern found in the Carpathian part of the Czech Republic was similar to that in Slovakia, with tetraploids at the higher altitudes. The distribution in the Herzynian part (Bohemian Massif) was just the opposite: the tetraploids were more often found at lower altitudes than the penta- and hexaploids. Both tetra- and pentaploid cytotypes occurred in a wide and similar spectrum of habitats, while hexaploids were limited to human-influenced habitats. A local-scale distribution of cytotypes analysed in detail in the Slovak Karst area, showed surprising differences in the distribution of cytotypes on particular karst plains, which can be related to different land uses. Concerning the contrasting altitudinal differentiation of tetraploids in the regions compared, the results suggest that at least two different types of tetraploids occur in Central Europe. The apparent cytotype diversity in the surrounding Slovak Karst area may suggest the existence of a primary contact zone.