Sex and gender are commonly thought to be synonymous, and both are generally classified using the binary categories of male and female. Existing standards applying to electronic health records (EHRs) all use, or until very recently have used, only these two categories plus “unknown” or “not-specified” with the latter options existing more for irretrievable or absent information than for purposes of documenting a diverse set of possible expected answers. Evidence is mounting that the binary options may not be adequate for many populations, including but not limited to intersex and transgendered patients. This paper examines the supporting basis for more inclusive and clear gender and sex classifications in EHRs, provides an argument that Meaningful Use Stage 3 should include a requirement for such a classification scheme, and proposes a framework for such requirements that would meet the needs of the affected population, providers, and vendors taking into account the experiences gathered by trailblazing providers and vendors since the IoM report of 2011.