Increasingly, EHR data are being used for clinical research study and patient-oriented interventions to address women’s health, sex and gender differences. At MGB, EHR data are also linked to MGB Biobank samples, which may be used for translational and mechanistic study. Data quality regarding gender and sex should therefore be of paramount concern to researchers. While there is a strong literature on gender field implementation best practices, a post-implementation, longitudinal assessment of gender demographic field use is lacking, highlighting a knowledge gap for research and care of gender diverse populations. Our study addresses this gap. In doing so, we identified potential data quality concerns and system-level vulnerabilities in gender demographic data that may impact research efforts to incorporate sex and gender as research variables as well as patient safety. More broadly, the user-level trends may inform system interoperability initiatives and provider- and patient-level education and training regarding sex and gender.