This study was conducted to evaluate the effects of dietary protein soybean meal (SBM) and cottonseed meal (CSM) sources and Amino Acid (AA) balances on performance, intestinal permeability and morphology in broiler chickens. Five hundred and twenty broiler chickens were fed an experimental diet from 21-42 days of age. A completely randomized block design was used with four treatments of SBM+CSM with AA Balance (B) and Imbalance (I) (SBM_B and SBM_I, SBM+CSM_B and SBM+CSM_I) were replicated 10 times with 13 broiler chickens per replicate. All respective treatments were kept in the same condition provide the diet twice a day and access to water ad libitum. The results showed that Daily Weight Gain (DWG), Daily Feed Intake (DFI), feed efficiency, Feed Conversion Ratio (FCR), carcass yield and dressing percentage were improved with SBM_B in comparison with all treatments. Furthermore, SBM_B significantly increased most of morphological findings in the intestinal parts studied. Intestinal permeability was (p<0.05) increased in SBM_I and SBM+CSM_I treatments. It is concluded that the best performance indices could be obtained by using SBM_B carcasses and morphological findings in comparison with other treatments.