This paper presents the development of the Machinery Risk Analysis (MRA) methodology for different ship machinery. This study is part of INCASS (Inspection Capabilities for Enhanced Ship Safety) FP7 EU funded research project, which tackles the issue of ship inspection and maintenance by accessing information related to ship surveys and incorporate harmonized cooperation of maritime stakeholders in order to avoid ship accidents, promote maritime safety and protect the environment. In this study, different systems are considered together with associated failure modes. The innovation of MRA is the consideration of multiple systems, sub-systems and components as well as failure interdependencies providing a holistic view of the reliability performance. Furthermore, MRA takes into account the system’s dynamic change of state, involving failure rate variation within time. The presented methodology involves the generation of a Markov Chain model integrated with the advantages of Bayesian Belief Networks (BBNs) developed in Java programming language