Matrix organization model is a sophisticated structure intended to combine both the efficiency and effectiveness of the functional and the product/service/customer/area dimensions. From the moment it was introduced in practice, this organizational architecture was accepted with enthusiasm, because it represented a complex organizational response adequate to the conditions which most of the companies in the world have been facing since 1970s. Although matrix organization is not a novelty, it is still a controversial model of organization design. The aim of this paper is to provide a deeper insight into the causes and effects of organizational misfits which appear in the implementation phase of three-dimensional matrix organization, as well as to offer some practical recommendations for managers on how to improve their capacities for successful management of complex matrix organization architecture in their organizations.