Abstract. 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 Salmonella and E. coli 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.