Dimensional control has a significant impact on overall product quality and performance of large and complex multistation assembly systems. To date, the identification of process-related faults that cause large variations of key product characteristics (KPCs) remains one of the most critical research topics in dimensional control. This paper proposes a new approach for multiple fault diagnosis in a multistation assembly process by integrating multivariate statistical analysis with engineering models. The proposed method is based on the following steps: (i) modeling of fault patterns obtained using state space representation of process and product information that explicitly represents the relationship between process-related error sources denoted by key control characteristics (KCCs) and KPCs, and (ii) orthogonal diagonalization of measurement data using principal component analysis (PCA) to project measurement data onto the axes of an affine space formed by the predetermined fault patterns. Orthogonal diagonalization allows estimating the statistical significance of the root cause of the identified fault. A case study of fault diagnosis for a multistation assembly process illustrates and validates the proposed methodology.