We describe an Early Warning System (EWS) which enables the root cause analysis for initiating quality improvements in the manufacturing shop floor and process engineering departments, at product OEMs as well as their tiered suppliers. The EWS combines the use of custom designed domain ontology of manufacturing processes and failure related knowledge, innovative application of domain knowledge in the form of probability constraints and a novel two step constrained optimization approach to causal network construction. Probabilistic reasoning is the main vehicle for inference from the causal network. This inference engine provides the capability to do a root cause analysis in manufacturing scenarios, and is thus a powerful weapon for an automotive EWS. This technique is widely applicable and can be used in various contexts in the broader manufacturing industry as well.