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Single-sex STEM programs have experienced increased popularity and scrutiny in recent years; prior studies on efficacy have been inconclusive. Through multiple regression models of survey responses from a nationally representative set of 15,725 US undergraduates, we show that attending single-sex programs is associated with a closing of gender gaps in STEM interest and STEM identity. Girls who attend all-girls programs have more long-term STEM career intention, while boys who attend all-boys programs are as closed off to STEM careers as boys who attend no program. Overall, single-sex programs seem to provide gains for girls while having mixed effects on boys. We discuss implications on STEM program funding, evaluation, and study.