Background: The Aetiology of Neonatal Infection in South Asia (ANISA) study is a population-based study with sites in Bangladesh, India and Pakistan. It aims to determine community-acquired incidence, etiology and associated risk factors for neonatal infections. Matiari, a rural site in Pakistan, was chosen for the study due to its high neonatal mortality rate and the presence of an established pregnancy and birth surveillance system. This article summarizes various challenges, remedial measures taken and lessons learned during the implementation of the ANISA study protocol in the unique rural setting of Matiari where the majority of births take place at home and accessibility to health care is limited.CHALLENGES: Achieving and maintaining ...