There is concern among Aboriginal communities in Canada that conventional approaches to the treatment of diabetes are ineffective in part because they fail to recognize the local Aboriginal perspective on the causal determinants of diabetes. While this shortcoming has been recognized, there have been no explicit attempts to practically define these perspectives and prescribe how conventional health management might be altered to incorporate them. In part, this may be due to difficulties in communicating Aboriginal perspectives in a manner which permits incorporation into conventional science-based frameworks. Here we use fuzzy cognitive mapping (FCM) as a technique to represent and compare Canadian Aboriginal and conventional science perspectives on the determinants of diabetes as contained in published articles drawn from a search of Medline and PubMed (1966-2005). The FCM allows for a detailed description of the complex system of culture, spirituality and balance at the root of the Aboriginal view. It also highlights how, for these less tangible factors, it is possible to identify more concrete stressors and outcomes which are amenable to management and monitoring. This preliminary comparison of conventional and Aboriginal views also demonstrates the potential for FCM as a technique to extract, compare and integrate perspectives of different knowledge systems into health management and policy development.