Abstract There is increasing media spotlight on gender bias against women in multiple facets of everyday life, due to the way in which data about individuals is gathered. We discuss how, in primary care, data used in clinical care and research is probably not inherently biased against women but instead, how bias may arise through data interpretation and application. We contrast this with the situation for transgender and intersex populations, where appropriate data collection is lacking, and improved guidance is needed on how to utilise risk scores and algorithms incorporating sex or gender. An awareness of these complexities and how they might be overcome will be essential for primary care clinicians to avoid exacerbating healthcare inequalities in this an increasingly data driven world.