Indigeneity is a complex social construct that can be defined in multiple ways using diverse markers traditionally based on the characteristics of individuals. Survey-based studies have used language, self-identification or location information to operationalise indigeneity. Yet, as suggested by Walters and Andersen (2013), Gillborn et al. (2018) and others, few scholars reflect on how the indigeneity variable is specified and whether this operationalisation may impact results. This paper examines this issue empirically using the case of indigeneity in Peru. First, survey-based empirical studies are identified to explore the ways in which indigeneity has been operationalised. Then, using the Young Lives study we present diverse operationalisations of indigeneity and outline how these may lead to different educational outcomes for children. We show that quantitative researchers using survey-based data should engage more deeply with different operationalisation of indigeneity as these can lead to different educational outcomes for children categorised as Indigenous.