Health systems world wide are confronted by the challenge of rising levels of chronic diseases. Yet existing approaches to health system analysis often fail to capture the complexity of the responses required to address this challenge. In this paper we describe the results of a pilot study using a rapid appraisal technique to assess the performance of the health care system in Kyrgyzstan, a former Soviet central Asian republic. The study focuses on diabetes, a condition whose effective management requires a coordinated response involving many components of the health care system. The study sets out a conceptual framework in which the system is seen from the perspectives of users, health professionals and policy-makers. It sees the effective delivery of health care as dependent on appropriate investment in human, physical, intellectual and social resources. The study reveals important weaknesses in all of these areas, although it also notes that current policies, while constrained by the legacy of the past and by limited resources, are beginning to tackle them. This pilot study indicates that rapid appraisal, using a condition such as diabetes, where those affected can be easily identified, offers a means of gaining important insights into a health care system.