Objectives. To examine the relationship between city-level structural stigma pertaining to sexual orientation and gender identity (SOGI) and completeness of patient SOGI data collection at US federally qualified health centers (FQHCs). Methods. We used the Human Rights Campaign's Municipal Equality Index to quantify city-level structural stigma against sexual and gender minority people in 506 US cities across 49 states. We ascertained the completeness of SOGI data collection at FQHCs from the 2018 Uniform Data System, which describes FQHC patient demographics and service utilization. We included FQHCs in cities captured by the structural stigma index in multinomial generalized linear mixed models to examine the relationship between city-level structural stigma and SOGI data completeness. Results. FQHCs in cities with more protective sexual orientation nondiscrimination policies reported more complete patient sexual orientation data (adjusted odds ratio [AOR] = 1.6; 95% confidence interval [CI] = 1.2, 2.1). This association was also found for gender identity nondiscrimination policies and gender identity data collection (AOR = 1.7; 95% CI = 1.3, 2.2). Conclusions. Municipal sexual and gender minority nondiscrimination laws are associated with social and municipal environments that facilitate patient SOGI data collection.(Am J Public Health. 2021;111(11):2059-2063. https://doi.org/10.2105/AJPH.2021.306414).