Antibiotics are recommended for use in the treatment of infectious diseases, but the side effects have not been thoroughly investigated, especially on the intestinal tract. Fluoroquinolones, macrolides and β-lactams were tested the side effects on the intestinal microbflora of mice in this study. The similarity and sequence analysis of the dominant bands for different drug administration periods were carried out by denaturing gradient gel electrophoresis (DGGE) profiles. The total amount of 16S rRNA gene increased after drug administration, the bacterial composition and structure could be divided into different clusters for different drug administration periods distinctly. This study revealed a significant change of bacterial composition of microflora from intestinal tract as antibiotics were applied to tested mice.