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Background  This article discusses our reflections on ethical and methodological challenges when conducting separate interviews with individuals in dyads in the uMkhanyakude district, South Africa. Our work is embedded in an ethnographic study exploring care relationships between adolescents and their older carers in the context of a large-donor funded HIV programme. We use these reflections to discuss some of the challenges and present possible management strategies that may be adopted in conducting dyadic health research in resource-poor settings.    Methods  Drawing from the relational agency, three rounds of separate interviews and participant observation were undertaken with dyads of adolescents aged between 13 and 19 and their older carers aged 50+ from October 2017 to September 2018. A reflexive journal was kept to record the interviewer's experiences of the whole research process. We identified methodological and ethical challenges from these data during the thematic analysis.    Results  A total of 36 separate interviews were conducted with six pairs of adolescent-older carer dyads ( n  = 12 participants). Five themes emerged: recruitment of dyads, consenting dyads, confidentiality, conducting separate interviews with adolescents and older carers, and interviewer-dyad interaction. We also illustrated how we dealt with these challenges.    Conclusions  Results from this study can guide the recruitment, consenting and collecting data for health studies that employ a similar form of enquiry in LMICs. However, ethical and methodological challenges should be recognised as features of the relationships between cross-generation dyads rather than weaknesses of the method.

A reflection on ethical and methodological challenges of using separate interviews with adolescent-older carer dyads in rural South Africa