Therapeutic proteins produced using recombinant DNA technologies are generally complex, heterogeneous, and subject to a variety of enzymatic or chemical modifications during expression, purification, and long-term storage. Hence the analytical strategies for characterization, quantitation, purity assay and evaluation of the biological activity of recombinant proteins still represent a big challenge and a matter for debate. The aim of the proposed special issue is to point out the main applications as well as future potentialities of the most advanced analytical techniques in the different aspects of the quality assessment of therapeutic proteins and in particular for conformation analysis, aggregates and impurities detection and quantitation, intact protein characterization, post-translational modifications (PTMs) identification and biological activity assessment. The special issue contains six in depth reviews and two original papers. Protein conformation is a key aspect to be assessed, because a specific conformation is essential for the biological function of the protein. The paper by Bertucci et al. points out the growing role of circular dichroism (CD) as a valuable and reliable technique to obtain this information, representing a useful tool for the study of pharmaceutical peptides themselves, in new formulations, after new processes of derivatization, production and storage. The paper also contains examples on the use of CD spectroscopy in the structural characterization of free and formulated recombinant proteins, looking at the prediction of the secondary structure, propensity to conformational changes, stability, and tendency to aggregation. Characterization of protein conformation by high resolution mass spectrometry (direct ESI-MS and hydrogen/ deuterium exchange) is reviewed by Bobst & Kaltashov. The paper provides an overview of the MS techniques and current trends for the characterization of the higher order structure and dynamics of biopharmaceutical products. Recombinant proteins often fail to reach their native conformation and in such cases they form different kinds of aggregates which are unsuitable for the intended applications. This has pressed, on one hand, the exploration of different approaches to favour protein folding, and on the other hand, the development of analytical strategies aimed at detecting soluble and insoluble aggregates. In the review by Garcia- Fruitos et al. the biological aspects of protein folding and unfolding are addressed together with an overview of the most advanced analytical techniques suitable for the fast evaluation of conformational quality and aggregation of recombinant drugs, even if showing apparent solubility.