This study consisted of two distinct research phases, performed within the context of the South African Council for Science and Industrial Research (and its current and potential research alliances). The purpose of the study was to develop a decision making model that would enable strategists at publicly financed research and development organisations to analyse and predict governance mode decisions, as well as select optimal governance mode structures (ranging from quasi-market structures, such as once-off contracts, to quasi-hierarchy structures, such as research joint ventures) for research alliances. During the qualitative first phase, the study aimed to identify impact domains within South Africa’s new Bayh-Dole-like Intellectual Property Rights legislative framework that consists of the Intellectual Property Rights from Publicly Financed Research and Development Act, as well as the Technology Innovation Agency Act, which could potentially influence research alliances (based on the Transactional Cost Economics, Resource-based View and Real Options Approach perspectives) with publicly financed research and development organisations. This was followed by the quantitative second phase, which attempted to verify the validity of a value-mediated governance mode model that included the highest ranked impact domains identified during the first phase as formative indicators for the perceived Intellectual Property Rights regime strength uncertainty factor. A qualitative online survey amongst senior managers at the Council for Science and Industrial Research, followed by Theme Extraction combined with Constant Comparative Method analysis, as well as a weighted frequency analysis, constituted the research methodology employed during the first phase’s identification and ranking of impact domains within the South African legislative framework. This phase demonstrated that the highest ranked impact domains (primarily driven by the Transactional Cost Economics perspective) included the choice of Intellectual Property Rights ownership, state walk-in rights on undeclared Intellectual Property, and benefit-sharing policies for the creators of Intellectual Property. The second phase consisted of a quantitative online survey, distributed amongst current and potential research alliance partners of the Council for Science and Industrial Research, followed by Structural Equation Modelling of a value-mediated governance model that included, amongst others, the perceived Intellectual Property Rights regime strength as an uncertainty factor. This phase revealed not only that the impact domains identified during the first phase could be used as formative indicators of the perceived Intellectual Property Rights regime strength, but also that stronger perceived regimes are positively related to the preference for quasi-hierarchy research alliance governance modes. Furthermore, it established that the expected value of a research alliance, which was shown to be positively influenced by the strength of the perceived Intellectual Property Rights regime, acted as a mediating factor on the relationship between the perceived Intellectual Property Rights regime strength and the preferred research alliance governance mode. Keywords: Bayh-Dole, Formative Indicators, Intellectual Property Rights, Research Alliances, Real Options Approach, Resource-based View, Quasi-Market Governance Modes, Quasi- Hierarchy Governance Modes, Structural Equation Modelling, Transactional Cost Economics, Value-mediated Governance Model. Copyright / Dissertation (MBA)--University of Pretoria, 2012. / Gordon Institute of Business Science (GIBS) / unrestricted