jats:pBackground: The large-scale quantitative evidence base to understand and improve health and healthcare outcomes for people who are trans and/or non-binary is still developing, although what research there is suggests that risk of poor health is high, and experiences of healthcare services are often poor. In 2021 the GP Patient Survey, which is carried out annually to measure patient experience in primary care in England, added inclusive questions about gender identity and trans status for the first time. Methods: This protocol paper pre-registers the methods that we will use for this work for a secondary analysis of these data, including both the statistical analysis protocol and early patient and public involvement work, to answer the following three research questions: (1) What are the (a) demographic characteristics, (b) health conditions, and (c) healthcare experiences of trans and/or non-binary adults in England? (2) Was there any difference in whether people who are trans and/or non-binary had been asked to shield during the COVID-19 pandemic or not compared with all other survey responders? (3) Does the relationship between being trans and/or non-binary, and self-reported long-term mental health problems, autism and autistic spectrum disorder and learning disability vary by age, gender, ethnicity, deprivation, sexual orientation or region?</jats:p>