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Abstract Background Paediatric research in low-income countries is essential to tackle high childhood mortality. As with all research, consent is an essential part of ethical practice for paediatric studies. Ethics guidelines recommend that parents or another proxy provide legal consent for children to participate, but that children should be involved in the decision through providing assent. However, there remain uncertainties about how to judge when children are ready to give assent and about appropriate assent processes. Malawi does not yet have detailed guidelines on assent. Understanding perspectives among children and their parents can assist in developing contextually-appropriate assent guidance. Methods Qualitative research was conducted with children and parents in three settings in Southern Malawi (low- and high-income urban and rural), to take account of any variations between socioeconomic and cultural contexts. In each setting, interviews were conducted with parents and their children who had participated in paediatric research to understand their experiences of assent and views on appropriate assent practice. Focus groups were also conducted with children and parents, to understand broader social perspectives. Results We found widespread support for involving children in decisions on research participation. Participants identified a range of factors that affect children’s capacity to give assent, including intellectual capacity, emotional development, life experience and cultural norms. Age was often mentioned as a consideration, but deemed an unreliable sole indicator of capacity to assent. In relation to appropriate assent processes, participants emphasised considerations such as supporting effective understanding and minimizing harms. Views on how to achieve these aims varied; for example, there were different ideas about the appropriate order in which to approach children and parents, and about whose decision to respect in the event of disagreement. Conclusions Parents and children agreed about the value of involving children in decisions on research, and about the need to promote children’s decision-making capacity while respecting parents’ interests in children’s welfare. Developing practical guidance that meets these principles is challenging, particularly given the need for flexible approaches that suit different study types, children’s capacities and family environments. Further discussion within the Malawi research and ethics community will help develop contextually-appropriate guidelines.