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Both a same-sex sexual orientation and gender nonconformity have been linked with poorer well-being; however, sexual orientation and gender nonconformity are also correlated. It is, therefore, critical to investigate their independent contributions to well-being. Based on survey responses of 230 female and 245 male high school seniors, the present study is one of the first to provide empirical data on this topic. Both childhood and adolescent gender nonconformity were negatively related to well-being. In the same analyses, neither sexual orientation nor biological sex was a significant predictor of well-being. These results suggest that gender-atypical traits may be more relevant for psychological health than a same-sex sexual orientation. Both environmental and biological influences may account for these findings.