Transgender (Trans, Trans*) persons may have a gender identity and a preferred name that differ from those assigned at birth, and/or those listed on their current legal identification (Gender ID, Birth-assigned Sex, Legal Sex). Transgender people who are referred to in a clinical setting using the wrong pronoun or name may suffer distress, ridicule or even assault by others in the waiting area, and may not return for further care. Furthermore, failure to accurately document (and therefore count) transgender identities has negative implications on quality improvement and research efforts, funding priorities and policy activities. The recent announcement that gender identity data may be included in Meaningful Use Stage 3 has accelerated the need for guidance for both vendors and local implementation teams on how to best record and store these data. A recent study demonstrated wide variation in current practices. This manuscript provides a description of identifiers associated with gender identity, and makes practical and evidence based recommendations for implementation and front-end functionality.