Nowadays, genetically modified plants are cultivated in many countries and it is important to consider their safety for surrounding environment. So, the environmental risk assessments of genetically modified plants are evaluated. This assessment consists of an objective evaluation of risk and involves generating; collecting and assessing of information on a GM plant with the aim to determine its impact on human or animal health and the environment relative to non-genetically modified organisms. One of the numerous methods used to investigate the impact of GM plants on the environment is the Terminal Restriction Fragment Length Polymorphism. This method was used for comparison of genetic variation in populations of bacteria isolated from rhizosphere of genetically modified maize MON810 carrying the gene cry1Ab and genetically non-modified maize. Rhizosphere samples were collected in Slovakia during two years (2008, 2009) in July and September and 16S rRNA gene was amplified from metagenomic DNA using universal eubacterial primers. Differences in the number of terminal restriction fragments between control and GM maize hybrids were not detected. Additionally, variation within bacterial communities composition from rhizosphere of MON810 and non-GM hybrids was not observed, nevertheless negligible differences in composition of bacterial community were observed between two sampling periods (July and September). These changes were observed in non-GM as well as in GM maize hybrids and reflected effects of environment and conditions, no influence of genetic modification. The 16S rDNA clone library creation from rhizosphere sample of MON810 maize followed by DNA sequencing revealed that the Proteobacteria were major group of bacteria and Actinobacteria, Firmicutes, and Chloroflexi were less represented. This study did not confirm any changes in the soil ecosystem, which would have been larger than normal variations caused by external conditions.