Background: All aspects of the heath care sector are being asked to account for their performance. This poses unique challenges for local public health units with their traditional focus on population health and their emphasis on disease prevention, health promotion and protection. Reliance on measures of health status provides an imprecise and partial picture of the performance of a health unit. In 2004 the provincial Institute for Clinical Evaluative Sciences based in Ontario, Canada introduced a public-health specific balanced scorecard framework. We present the conceptual deliberations and decisions undertaken by a health unit while adopting the framework.