Adaptive hpq finite element methods for the analysis of 3D-based models of complex structures. Part II: A posteriori error estimation. This is the second paper out of a series of papers devoted to model- and hpq-adaptive finite element methods assigned for the modeling and analysis of elastic structures of complex mechanical description. In our previous publication [G. Zboinski, Comput. Methods Appl. Mech. Eng. 199, No. 45–48, 2913–2940 (2010; Zbl 1231.74449)]we investigated the issue of hierarchical models and approximations of such structures. We applied 3D or 3D-based mechanical models, hierarchical modeling, and hierarchical approximations within the proposed finite element formulation. Furthermore, we assumed that the mechanical model and discretization parameters (such as: the size h of the element, and the longitudinal and transverse approximation orders, p and q) could vary locally, i.e. they could be different in each finite element. The a posteriori error estimation discussed in the present paper is based on the generalization of the residual equilibration method on the models with internal constraints. The generalized method is applied to the assessment of the total and approximation errors, while the modeling error is calculated as the difference between the former two errors. The corresponding error-controlled adaptive procedures are based on a three-step strategy, with possible iterations of h- and p-steps.