Lesbian, gay, bisexual, and transgender (LGBT) individuals in U.S. workplaces often face disadvantages in pay, promotion, and inclusion and emergent research suggests that these disadvantages may be particularly pernicious within science and engineering environments. However, no research has systematically examined whether LGBT employees indeed encounter disadvantages in science, technology, engineering and math (STEM) organizations. Using representative data of over 30,000 workers employed in six STEM-related federal agencies (the Department of Energy, the Environmental Protection Agency, the National Science Foundation, NASA, the Nuclear Regulatory Commission, and the Department of Transportation), over 1000 of whom identify as LGBT, we compare the workplace experiences of LGBT employees in STEM-related federal agencies with those of their non-LGBT colleagues. Across numerous measures along two separate dimensions of workplace experiences-perceived treatment as employees and work satisfaction-LGBT employees in STEM agencies report systematically more negative workplace experiences than their non-LGBT colleagues. Exploring how these disadvantages vary by agency, supervisory status, age cohort, and gender, we find that LGBT persons have more positive experiences in regulatory agencies but that supervisory status does not improve LGBT persons' experiences, nor do the youngest LGBT employees fare better than their older LGBT colleagues. LGBT-identifying men and women report similar workplace disadvantages. We discuss the implications of these findings for STEM organizations and STEM inequality more broadly.