BackgroundIntegrated Management of Childhood Illness (IMCI) and Emergency Triage, Assessment and Treatment (ETAT) are guidelines developed by the World Health Organization to reach targets for reducing under-5 mortality. They were set out in the Millennium Development Goals. Each guideline was established separately so the purpose of this study was to understand how these systems have been integrated in a primary care setting and identify barriers and facilitators to this integration using a systems approach.MethodInterviews were carried out with members of staff of different levels within a primary healthcare clinic in Malawi. Along with observations from the clinic this provided a well-rounded view of the running of the clinic. This data was then analysed using the SEIPS 2.0 work systems framework. The work system elements specified in this model were used to identify and categorise themes that influenced the clinic’s efficiency.ResultsA process map of the flow of patients through the clinic was created, showing the tasks undertaken and the interactions between staff and patients. In their interviews, staff identified several organisational elements that served as barriers to the implementation of care. They included workload, available resources, ineffective time management, delegation of roles and adaptation of care. In terms of the external environment there was a lack of clarity over the two sets of guidelines and how they were to be integrated which was a key barrier to the process. Under the heading of tools and technology a lack of guideline copies was identified as a barrier. However, the health passport system and other forms of recording were highlighted as being important facilitators. Other issues highlighted were the lack of transport provided, challenges regarding teamwork and attitudes of members of staff, patient factors such as their beliefs and regard for the care and education provided by the clinic.ConclusionsThis study provides the first information on the challenges and issues involved in combining IMCI and ETAT and identified a number of barriers. These barriers included a lack of resources, staff training and heavy workload. This provided areas to work on in order to improve implementation.