In the last years, the spread of computers and the Internet caused a significant amount of documents to be available in digital format. Collecting them in digital repositories raised problems that go beyond simple acquisition issues, and cause the need to organize and classify them in order to improve the effectiveness and efficiency of the retrieval procedure. The success of such a process is tightly related to the ability of understanding the semantics of the document components and content. Since the obvious solution of manually creating and maintaining an updated index is clearly infeasible, due to the huge amount of data under consideration, there is a strong interest in methods that can provide solutions for automatically acquiring such a knowledge. This work presents a framework that intensively exploits intelligent techniques to support different tasks of automatic document processing from acquisition to indexing, from categorization to storing and retrieval. The prototypical version of the system DOMINUS is presented, whose main characteristic is the use of a Machine Learning Server, a suite of different inductive learning methods and systems, among which the more suitable for each specific document processing phase is chosen and applied. The core system is the incremental first-order logic learner INTHELEX. Thanks to incrementality, it can continuously update and refine the learned theories, dynamically extending its knowledge to handle even completely new classes of documents. Since DOMINUS is general and flexible, it can be embedded as a document management engine into many different Digital Library systems. Experiments in a real-world domain scenario, scientific conference management, confirmed the good performance of the proposed prototype.