From 2002 onwards, the Ludwig Boltzmann Gesellschaft underwent modernisation within the scope of a comprehensive reform. The reform contributed to overcoming its division into small sections and the predominantly short-term orientation of the research, as well as intensifying the cooperation between research-offering establishments and research-using organisations and providing for this on a solid institutional basis. It was the aim of this reform to make the LBG into a research-promoting organisation which corresponds to international standards not only in terms of its content but also in terms of its structure. In particular, the introduction of coherent and transparent calls for proposals and evaluation processes were at the forefront of these developments .

This reform brought about – alongside the content-related focus on humanities, social and cultural sciences as well as human medicine, clinical research and life sciences – a significant reduction in the number of Institutes. Of the 135 Institutes existing in 2002, 90 Institutes with predominantly small divisions had ceased their research activities following a fundamental evaluation at the end of 2005. Following the recommendations of the evaluation, some of the positively evaluated Institutes were continued and some were brought together into thematic clusters. LBIs which were dedicated to related research matters were thereby asked to submit proposals for joint programmes. It was thus possible to transform the subject-related Institutes into clusters pursuing common goals and being outwardly represented as a single body. The Institutes forming the respective clusters still exist today.