A greenhouse experiment was carried out with transgenic potato plants expressing the antibacterial lytic peptide cecropin in order to determine whether non-target Bacillus communities in the rhizosphere are affected by such plants. Two cecropin expressing lines, a line containing only vector sequences and the parental variety Achirana Inta (AI) were included in the experiment. At the flowering and the tuber production stage a total of 621 Bacillus isolates was obtained from the potato rhizospheres, and strains were analysed by PCR?RFLP analysis of the 16S rRNA gene and the 16S?23S rDNA intergenic spacer. Representative isolates were further analyzed by partial 16S rDNA sequence analysis. At the flowering stage the cecropin expressing lines caused a transient, but significant effect on the diversity and community structure of culturable Bacillus spp. Populations associated with the plasmid-containing potato line showed diversity values comparable to the Bacillus communities found in the rhizospheres of wildtype plants, but community structures were highly different. At the tuber production stage the rhizosphere Bacillus populations showed only few differences. The observed effects can be partly explained by different sensitivities of the Bacillus community members towards cecropin. In addition, unintentionally altered plant characteristics seem to be responsible for the different population structures found in the rhizospheres of transgenic plants