There is growing interest in health systems research and implementation studies within public health, yet there is little in-depth research being carried out on the front-line health workers who implement interventions in the field. This study aims to add to our understanding of implementation processes through an in-depth ethnographic study conducted over a 12 month period of participant observation with field-level health workers in an urban leprosy project. The study employs a multidisciplinary approach, combining anthropological and public health methods and perspectives, and was carried out within one of India's largest leprosy organisations. The research is, in essence, a 'project ethnography' of the work and social identity of health workers, within the context of a rapidly changing policy landscape. The study argues that health workers are embedded in the structures they work within at the same time as they actively exercise agency within these structures. By understanding how health workers utilise agency within, rather than in opposition to, structure, we can come to understand health workers' social identity, as well as how they reconcile organisational intent with local strategies in the implementation process. There is a growing realisation within public health that health systems are complex social microcosms in which health workers play a pivotal role. The study argues that the application of social theory, that examines the relationship between agency and structure, will be instrumental in developing research frameworks that truly engage with the process and complexity of health systems.