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In this paper, a methodology based on Bayesian Network (BN) was proposed to deal with the difficulty of risk analysis in RoPax transport. Based on data collection and expert survey, BN model for RoPax sailing risk analysis was constructed first. Then the Expectation Maximization (EM) algorithm for parameter learning and Evidence Prepropagation Importance Sampling (EPIS) algorithm for reasoning were designed. Finally, a sensitivity analysis was conducted. To validate the model algorithms, a case study on the RoPax system of Bohai gulf in China was provided. Results indicate that the BN model can effectively address the problem of data deficiency and mutual dependency of incidents in risk analysis. It can also model the development process of unexpected hazards and provide decision support for risk mitigation. First published online: 10 Sep 2014