The 1992-95 war in Bosnia-Herzegovina created deep ethnic divisions in alreadyfragmented university structures, where individual faculties possessed considerable academic and financial independence. The faculties, in turn, in the Humboldtian tradition, were composed of semi-autonomous "chairs" and institutes. This level of the organisation had gained added autonomy in the Communist period from the distinctive Yugoslav "self-management" principle, intended to empower operating units. This fragmentation at institutional level is compounded in present-day Bosnia-Herzegovina by the absence of any effective national-level planning and control of higher education. Post-war reform efforts by international agencies have addressed some of the problems of this fragmented structure. But they have not taken sufficient account of the differences between the academic principles on which the universities of Bosnia-Herzegovina are founded and those of the Anglo-American tradition, from which models of managerial reform are typically taken. Through a better understanding of the universities' long-established organisational frameworks, it may be possible for aid projects to help achieve enhanced institutional managerial effectiveness and to reverse some of the more damaging effects of multi-level fragmentation.