The present study was planned to investigate the effect of different levels of chlorine dioxide on the performance, gut microbiota and intestinal histology of quails. For this purpose, 300 day-old healthy quail chicks were randomly placed in 20 specially designed pens (15 birds/pen) with water troughs containing chlorine dioxide at the level of 0.00 (DW-0.00), 0.3 (DW-0.3), 0.4 (DW-0.4) and 0.5 ppm (DW-0.5) in replicated fashion (5 replicate/treatment) for 28 days. Weight gain, feed conversion ratio and dressing percentage increased significantly (P<0.05) in DW-0.5 group. Similarly, liver, gizzard and heart weight increased significantly in treated groups linearly with increasing levels of treatment at day 21 and 28. The results showed that population of <i>Salmonella</i> and <i>E. coli</i> decreased linearly at day 21 and 28 of age. Villus height and goblet cells at day 21 and 28 were significantly higher in DW-0.5 group. The results of the present study suggested that the treatment of chlorine dioxide linearly increased the performance and gut morphology and decreased microbial population in quails.