The aim of the study was to analyse selected aspects of the natural variability of selected varieties of Vitis vinifera. Grapevine is one of the most popular and desirable crops in the world due to the great tradition of wine production, but grape extracts also have a wide range of pharmaceutical effects on the human body. It is important to identify different varieties for the conservation of genetic resources, but also for commercial and cultivation purposes. The variability of conserved DNA-derived polymorphism profiles, as well as microbial characteristics, were analysed in this study. Six different varieties of Vitis vinifera L. were used in the study: Cabernet Savignon, Chardonney, Welschriesling, Weisser Riesling, Gewurztramines and Gruner Veltliner. Genetic polymorphism was analysed by CDDP markers for WRKY genes. Polymorphic amplicon profiles were generated by all primer combinations used in the study. Gruner Veltliner and Welschriesling were the most similar, with a similarity value at 0.778. Microbiological quality of grape and antimicrobial activity against Gram-positive and Gram-negative bacteria and yeasts were analysed further. The plate diluting method for microbial quality and the disc diffusion method for antimicrobial activity were evaluated. The number of total count of bacteria ranged between 3.12 in Cabernet Sauvignon to 3.62 log cfu/g in Grűner Veltliner. The best antimicrobial activity showed Gewurztramines against Salmonella enterica, Yersinia enterocolitica, Pseudomonas aeroginosa, Staphylococcus aureus, Listeria monocytogenes, Candida albicans, Candida krusei, and Candida tropicalis. The best antimicrobial activity was found against Enterococcus faecalis in variety Weisser Riesling.