The 2011 Institute of Medicine report on LGBT health recommended that sexual orientation and gender identity (SO/GI) be documented in electronic health records (EHRs). Most EHRs cannot document all aspects of SO/GI, but some can record gender of sexual partners. This study sought to determine the proportion of patients who have the gender of sexual partners recorded in the EHR and to identify factors associated with documentation. A retrospective analysis was done of EHR data for 40 family medicine (FM) and general internal medicine (IM) practices, comprising 170,570 adult patients seen in 2012. The primary outcome was EHR documentation of sexual partner gender. Multivariate logistic regression assessed the impact of patient, provider, and practice factors on documentation. In all, 76,767 patients (45%) had the gender of sexual partners recorded, 4.3% of whom had same-gender partners (3.5% of females, 5.6% of males). Likelihood of documentation was independently higher for women; blacks; those with a preventive visit; those with a physician assistant, nurse practitioner, or resident primary care provider (vs. attending); those at urban practices; those at smaller practices; and those at a residency FM practice. Older age and Medicare insurance were associated with lower documentation. Sexual partner gender documentation is important to identify patients for targeted prevention and support, and holds great potential for population health management, yet documentation in the EHR currently is low. Primary care practices should routinely record the gender of sexual partners, and additional work is needed to identify best practices for collecting and using SO/GI data in this setting.