Many organizational contexts should be considered in designing EDI controls to make control systems effective and efficient. This paper gives a description of the neural network model for suggesting the extent of effective EDI controls for a company that has specific organizational environment. Feedforward backpropagation neural network models are designed to predict the state of 12 modes of EDI controls from the state of environment. The predictive power of the system is compared with that of multivariate regression analysis to evaluate the effectiveness of using neural network model in predicting the level of EDI controls. The results show that the neural network model outperforms regression analysis in predictive accuracy. The controls that have high estimated value in the model are likely to be critical controls and EDI auditor or management can enhance investment of IS resources to enhance these controls.