Emerging infectious diseases regained substantial international attention in recent years and it has been argued that flexibility and innovation in public health systems is needed in order to react to changing challenges. This paper will take these policy claims as a starting point to examine the case of multi-drug resistant Tuberculosis (MDR-TB) in India. Based on fieldwork results it will be examined how the existing control efforts of TB in India respond to the emergence of MDR-TB, what solutions are discussed for diagnosing, treating and preventing MDR-TB and what can be learned from that with regard to innovation and flexibility of a public health system in a country like India. The discussions and reactions to MDR-TB indicate that arguments for flexibility meet constraints of the existing control system and the Indian public health and wider social system. However, the flexibility that is argued for goes beyond what has been envisaged in international policy arenas (mainly focusing on preparation of various capacities in surveillance, detection and research). Rather it involves localized learning and experimenting within existing control structures that are claimed to have become too rigid in trying to keep up quality standards faced with a weakening public health system. Furthermore, the case shows that existing challenges in TB control resurface with the emergence of MDR-TB and reflect a difficult balancing act between biomedical values, socio-cultural values and operational feasibility. However, various actors are striving for change and it is in these instances that one can start to understand what flexibility and innovation could mean for a public health challenge such as TB in India. The paper concludes with an argument for a detailed analysis of these changes from an innovation perspective.