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Introduction: There is growing interest in health system performance and recently WHO launched a report on health systems strengthening emphasising the need for close monitoring using system-wide approaches. One recent method is the balanced scorecard system. There is limited application of this method in middle- and low-income countries. This paper applies the concept of balanced scorecard to describe the baseline status of three intervention districts in Zambia. Methodology: The Better Health Outcome through Mentoring and Assessment (BHOMA) project is a randomised step-wedged community intervention that aims to strengthen the health system in three districts in the Republic of Zambia. To assess the baseline status of the participating districts we used a modified balanced scorecard approach following the domains highlighted in the MOH 2011 Strategic Plan. Results: Differences in performance were noted by district and residence. Finance and service delivery domains performed poorly in all study districts. The proportion of the health workers receiving training in the past 12 months was lowest in Kafue (58%) and highest in Luangwa district (77%). Under service capacity, basic equipment and laboratory capacity scores showed major variation, with Kafue and Luangwa having lower scores when compared to Chongwe. The finance domain showed that Kafue and Chongwe had lower scores (44% and 47% respectively). Regression model showed that children's clinical observation scores were negatively correlated with drug availability (coeff −0.40, p = 0.02). Adult clinical observation scores were positively association with adult service satisfaction score (coeff 0.82, p = 0.04) and service readiness (coeff 0.54, p = 0.03). Conclusion: The study applied the balanced scorecard to describe the baseline status of 42 health facilities in three districts of Zambia. Differences in performance were noted by district and residence in most domains with finance and service delivery performing poorly in all study districts. This tool could be valuable in monitoring and evaluation of health systems. [ABSTRACT FROM AUTHOR]