This paper presents a novel fault detection approach for industrial batch processes. The batch processes under consideration are characterized by the interaction between discrete system modes and non-stationary continuous dynamics. Therefore, a stochastic hybrid process model (SHPM) is introduced, where process variables are modeled as time-variant Gaussian distributions, which depend on hidden system modes. Transitions between the system modes are assumed to be either autonomous or to be triggered by observable events such as on/off signals. The model parameters are determined from training data using expectation-maximization techniques. A new fault detection algorithm is proposed, which assesses the likelihoods of sensor signals on the basis of the stochastic hybrid process model. Evaluation of the proposed fault detection system has been conducted for a penicillin production process, with the results showing a significant improvement over the existing baseline methods.Note to Practitioners—Automatic fault detection makes it possible to limit the effects of faults by taking countermeasures at an early stage. In this work, a data-driven fault detection method for industrial batch processes is proposed, in which the underlying process model is learned from training data. The proposed fault detection system can be used for various industrial batch processes without the need for complex and error-prone manual configuration. In contrast to many other data-driven approaches such as neural networks, only a few process cycles are required to create a robust process model. It should be noted that in data-driven fault detection methods, the training data should cover a large part of the process states that occur during error-free process cycles. The developed method is therefore particularly suitable for cyclical processes, which, however, can have alternative process paths and variability between the process cycles.