Addressing the complex and longstanding relationship between universities and security and intelligence agencies, this article provides a tentative, working conceptual framework for research ethics in a global higher education environment. The article does so in the light of intensified threats of international terrorism which have brought this historic relationship to the contemporary foreground of academic life. Seeing higher education environments as part of a broader process of enhanced security in societies worldwide, we use securitization theory to provide an analytical framework specifically for understanding a complex of historical-contemporary relationships between universities and security and intelligence agencies. As the basis for framing the ethical issues which arise for researchers across all disciplines, the intention is to raise awareness of a relationship which by its very, especially historical, nature, has been secret. The article suggests identify a three-fold analytical framework were structural, operational and ethical considerations are interwoven in complex ways. At the structural level we identify three modus operandi (covert, overt, covert-overt); and four academic ethical principles (standards; freedom; engagement; conduct). While the conceptual framework presented makes no pretence of offering a complete or comprehensive picture of a complex and still evolving relationship, the intention is provide some critical balance and coherence to a contentious not to say often divisive aspect of research ethics in the securitised university.