This study was conducted to investigate the effect of Protexin on performance, some carcass traits and intestinal microbial population of Japanese quails. A total of 156 seven day quails were divided into 4 treatments and 3 replicates each. The treatments were basal diet without Protexin as control, 0.025, 0.050 and 0.100 g/ton Protexin respectively. During the experiment period feed intake (FI), body weight gains (BWG) and feed conversion ratio (FCR) were measured weekly. At the end of trial (56 days), 2 birds form each replicate were slaughtered for carcass and some visceral organs evaluation. In addition intestinal microbial population of Escherichia coli, Entrobacter and Bacillus colonies were investigated. Data showed that using of Protexin increased feed intake none significantly. Body weights and feed to gain ratio were improved significantly (P<0.05) in first, second and third weeks. There were no significant differences in visceral organs between treatments except liver percentage. The results suggested that using Protexin probiotic has positively changed intestinal Escherichia coli, Enterobacter and Bacillus compared to the control groups (P<0.05). It seems that inclusion of Protexin probiotic has a positive effect on performance and intestinal microflora in Japanese quails.