Within the last two years, respective proposals by the Scottish and UK Governments to reform the Gender Recognition Act 2004 (GRA) to allow people to change their legal sex based only on making a legally-registered self-declaration have sparked an intense debate on how sex and gender identity should be defined in law and policy. This paper examines how gender self-identification had in fact become a feature of Scottish policy-making and practice, long before public consultation on GRA reform began. The analysis is structured as two case-studies that examine firstly, policy development on the census in relation to the ‘sex’ question, and second, Scottish Prison Service policy on transgender prisoners. The analysis shows that the unregulated roll-out of gender self-identification in Scotland has taken place with weak or non-existent scrutiny and a lack of due process, and that this relates to a process of policy capture, whereby decision-making on sex and gender identity issues has been directed towards the interests of a specific interest group, without due regard for other affected groups or the wider population. The paper raises questions about the adequacy of institutional safeguards against well-organised and highly purposeful lobbying, particularly where any groups detrimentally affected do not have effective representation.