Organisational factors can affect the success of interventions aimed at increasing research use. Research is needed to identify organisational factors affecting research use in specific public health policy contexts. Qualitative interviews with decision makers from a specific public health context identified a range of organisational factors that affected policy and programme decision making. Interestingly, factors affecting decision making generally were comparable to factors that affect research use specifically, highlighting the complexity of policy and programme decision making. Results revealed a window of opportunity to frame increased research use as part of broader organisational change aimed at improving policy and programme development and outcome measurement.