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Background While there is widespread consensus that sex- and gender-related factors are important for how interventions are designed, implemented, and evaluated, it is not currently known how alcohol treatment research accounts for sex characteristics and/or gender identities and modalities. This methodological systematic review documents and assesses how sex characteristics, gender identities, and gender modalities are operationalized in alcohol treatment intervention research involving youth. Methods and findings We searched MEDLINE, Embase, Cochrane Central Registry of Controlled Trials, PsycINFO, CINAHL, LGBT Life, Google Scholar, Web of Science, and grey literature from 2008 to 2023. We included articles that reported genders and/or sexes of participants 30 years of age and under and screened participants using AUDIT, AUDIT-C, or a structured interview using DSM-IV criteria. We limited the inclusion to studies that enrolled participants in alcohol treatment interventions and used a quantitative study design. We provide a narrative overview of the findings. Of 8,019 studies screened for inclusion, 86 articles were included in the review. None of the studies defined, measured, and reported both sex and gender variables accurately. Only 2 studies reported including trans participants. Most of the studies used gender or sex measures as a covariate to control for the effects of sex or gender on the intervention but did not discuss the rationale for or implications of this procedure. Conclusions Our findings identify that the majority of alcohol treatment intervention research with youth conflate sex and gender factors, including terminologically, conceptually, and methodologically. Based on these findings, we recommend future research in this area define and account for a spectrum of gender modalities, identities, and/or sex characteristics throughout the research life cycle, including during study design, data collection, data analysis, and reporting. It is also imperative that sex and gender variables are used expansively to ensure that intersex and trans youth are meaningfully integrated. Trial registration Registration: PROSPERO, registration number: CRD42019119408, Author(s): A.J. Lowik 1,2, Caroline Mniszak 1,3, Michelle Pang 1, Kimia Ziafat 1,3, Mohammad Karamouzian 4, Rod Knight 1,5,6,* Introduction While there is widespread consensus that sex- and gender-based factors [...]