This paper addresses trajectory tracking control of port-controlled Hamiltonian systems via generalized canonical transformations and passivity-based control. The main strategy adopted in this paper is to construct an error system, which describes the dynamics of the tracking error, by a passive port-controlled Hamiltonian system. After obtaining the error system, tracking control of the original system can be achieved by stabilizing the error system via passivity-based approach. First, a fundamental framework is provided for constructing the error system via generalized canonical transformations. Then a concrete design procedure is derived for a class of electro-mechanical systems. Furthermore, the proposed method is applied to a magnetic levitation system and laboratory experiments demonstrate its effectiveness. (C) 2003 Elsevier Ltd. All rights reserved.