Fault isolation is known to be a challenging problem in machinery troubleshooting. It is not only because the isolation of multiple faults contains considerable number of uncertainties due to the strong correlation and coupling between different faults, but often massive prior knowledge is needed as well. This paper presents a Bayesian network-based approach for fault isolation in the presence of the uncertainties. Various faults and symptoms are parameterized using state variables, or the so-called nodes in Bayesian networks (BNs). Probabilistically causality between a fault and a symptom and its quantization are described respectively by a directed edge and conditional probability. To reduce the qualitative and quantitative knowledge needed, particular considerations are given to the simplification of Bayesian networks structures and conditional probability expressions using rough sets and noisy-OR/MAX model, respectively. By adopting the simplified approach, symptoms under multiple-fault are decoupled into the ones under every single fault, while the quantity of the conditional probabilities is simplified into the linear form of the faults quantity. Prior knowledge needed in Bayesian network-based diagnostic model is reduced significantly, which decreases the complexity in establishing and applying this diagnosis model. The computational efficiency is improved accordingly in the simplified BN model, after eliminating the redundant symptoms. The fault isolation methodology is illustrated through an example of diesel engine fuel injection system to verify the developed model.