Institutional research repositories are becoming more and more diffused means for the analysis of the research performance of Universities, besides international databases, as the Web of Science and more recently the Elsevier database Scopus, which have been widely used as sources for assessing the scientific productivity and to produce international bibliometric rankings.Institutional databases collect all academic outputs, which go beyond the traditional publications, such as articles in newspaper, exhibits, working papers, notes, letters, manuals, reports. So far, while international databases could be biased by a limited coverage of scientific products especially in some fields of science (i.e Social Sciences and Humanities), institutional datasets can provide a quite comprehensive insight into the scientific production of an academic institution and can be powerful sources to build indicators aiming at describing universities. UNIPUB project aims at assessing the extent to which they can be used to produce simple indicators of publications at the level of whole higher education institutions and scientific fields. The team of the project is composed of three research groups: CERIS CNR in Italy, the University of Lugano in Switzerland, IEDCYT and University Carlos III of Madrid, Spain. UNIPUB was one of the projects on Science Technology and Innovation Indicators developed within the PRIME Network of Excellence, VI European Framework Programme (http://www.prime‐noe.org). The purpose is to methodologically exploit institutional databases, and to build profiles of research activities of the Universities, rather than to evaluate quality of research, coherently with the positioning indicators rationale and with a policy orientation promoting the differentiation of higher education institutions according to different missions and social and geographical spaces, rather than their competition along the unique dimension of the international academic reputation. Positioning indicators, in fact, describe the position of an academic institution in its complex, fragmented and multidimensional institutional space and the characteristics of the institutions themselves, in our case the HEIs, their competitive behaviors, and their collaborations and linkages with other actors considered as important elements of their performance. So far the UNIPUB project, after a description of the institutional datasets of a sample of 5 universities in the partner countries (use, contents, bibliographic information and quality and updating procedures), has experimented the possibility to use them to develop and to test a set of five descriptors and three indicators that encompass scientific production differentiation, Universities mission, their regional, national and international orientation, collaborations and linkages with different actors and stakeholders. This Report presents the results of the analysis developed in Spain for two Universities: Universidad Carlos III de Madrid and Universitat de Barcelona. The discussion is not intended to address the issue of productivity and research performance; instead, it is devoted to put into evidence opportunities and methodological constraints of the existing databases and to present ways for improving them. A comparative analysis of the outcome in the three countries involved in the project is presented in the UNIPUB General Report, which also shows the results of a survey developed within the three countries involved, on the characteristics of the University institutional databases.