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The Russian Federation has the eleventh highest tuberculosis burden in the world in terms of the total estimated number of new cases that occur each year. In 2003, 26% of the population was covered by the internationally recommended control strategy known as directly observed treatment (DOT) compared to an overall average of 61% among the 22 countries with the highest burden of tuberculosis. The Director-General of WHO has identified two necessary starting points for the scaling-up of interventions to control emerging infectious diseases. These are a comprehensive engagement with the health system and a strengthening of the health system. The success of programmes aimed at controlling infectious diseases is often determined by constraints posed by the health system. We analyse and evaluate the impact of the arrangements for delivering tuberculosis services in the Russian Federation, drawing on detailed analyses of barriers and incentives created by the organizational structures, and financing and provider-payment systems. We demonstrate that the systems offer few incentives to improve the efficiency of services or the effectiveness of tuberculosis control. Instead, the system encourages prolonged supervision through specialized outpatient departments in hospitals (known as dispensaries), multiple admissions to hospital and lengthy hospitalization. The implementation, and expansion and sustainability of WHO-approved methods of tuberculosis control in the Russian Federation are unlikely to be realized under the prevailing system of service delivery. This is because implementation does not take into account the wider context of the health system. In order for the control programme to be sustainable, the health system will need to be changed to enable services to be reconfigured so that incentives are created to reward improvements in efficiency and outcomes.