This paper discusses the problem of risk estimate and choice of the rational variants in the transportation using expert information systems. The pairwise comparison method (Saaty’s method) is used to determine the weights of chosen criteria. An example is given that compares logistic risks in shipping, railway and aviation transport. The input data are taken in the example are formal and can be chosen for the concrete problems. This example is solved by both non-fuzzy and fuzzy approach. It is shown that with the set of data in the railway transport is the optimal option. The results demonstrate the efficiency of the proposed method.