The analysis of polymorphism between 46 maize inbred lines with known genetic background and the classification of these lines in related groups was carried out by means of morphological, isoenzyme and genetic markers. The degree of relationship between the lines was determined using cluster analysis. Only a very limited extent of allele polymorphism could be detected in isoenzyme analyses. Nevertheless, on the basis of RAPD and SSR markers, all the lines could be distinguished from each other. Grouping lines into related groups it was found that, while the individual marker systems only partially reflected the actual relationships, a joint analysis of genetic markers and morphological data revealed a close correlation between the groups formed on the dendrogram and genetic backgrounds.