Community-based interventions are an important way of improving health in low-income countries. A necessary prerequisite for the design of such interventions is an understanding of the local health system. This will inform intervention design, help ensure the community-intervention forms part of a continuum of care, and provide information about health system strengthening activities that may be necessary for success. Such formative research processes, however, are seldom reported in the literature. We present the results of a health facility assessment used in the design stage of Newhints, a community-based intervention to improve neonatal survival in rural Ghana. We illustrate the methodology, findings and how these were used to inform the design and implementation of Newhints. The assessment involved key informant interviews with staff members at seven health facilities within the study area, including a brief inventory of available drugs and equipment. The key informant interviews identified that practices and health promotion messages at the health facilities were not consistent with one of the key target behaviours of the Newhints intervention - thermal care through delayed infant bathing. Health workers were bathing neonates soon after delivery and also advising women to do the same, which is a potential cause of hypothermia for the newborn. We found that health centres other than large district hospitals were ill-equipped to treat serious complications of labour or illness in the newborn, which had implications for advice on health seeking behaviour within the intervention. As a result of the health facility assessment, it was deemed necessary to undertake both health worker training and sensitisation activities. We demonstrate that important information can be yielded from a relatively simple health facility assessment involving key informant interviews.