During last decade, machine learning and, in particular, statistical approaches have become more and more important for research in Natural Language Processing (NLP) and Computational Linguistics. Nowadays, most stakeholders of the field use machine learning, as it can significantly enhance both system design and performance. However, machine learning requires careful parameter tuning and feature engineering for representing language phenomena. The latter becomes more complex when the system input/output data is structured, since the designer has both to (i) engineer features for representing structure and model interdependent layers of information, which is usually a non-trivial task; and (ii) generate a structured output using classifiers, which, in their original form, were developed only for classification or regression. Research in empirical NLP has been tackling this problem by constructing output structures as a combination of the predictions of independent local classifiers, eventually applying post-processing heuristics to correct incompatible outputs by enforcing global properties. More recently, some advances of the statistical learning theory, namely structured output spaces and kernel methods, have brought techniques for directly encoding dependencies between data items in a learning algorithm that performs global optimization. Within this framework, this special issue aims at studying, comparing, and reconciling the typical domain/task-specific NLP approaches to structured data with the most advanced machine learning methods. In particular, the selected papers analyze the use of diverse structured input/output approaches, ranging from re-ranking to joint constraint-based global models, for diverse natural language tasks, i.e., document ranking, syntactic parsing, sequence supertagging, and relation extraction between terms and entities. Overall, the experience with this special issue shows that, although a definitive unifying theory for encoding and generating structured information in NLP applications is still far from being shaped, some interesting and effective best practice can be defined to guide practitioners in modeling their own natural language application on complex data.