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Introduction: Nearly 2 million youth experience homelessness each year in the U.S. Rates of comorbid substance use/mental health disorder are prevalent in this population, and may increase the physical and mental health consequences of homelessness. Self-medication may be one explanation for these high rates of comorbidity, but the self-medication hypothesis of substance use has not been studied among homeless youth. Methods: A sample of 448 homeless youth recruited from drop-in centers in Los Angeles, CA provided information on substance use, mental health, and self-medication as a motivator for substance use. Multivariable logistic regressions, controlling for demographic characteristics, assessed associations between these factors. Results: Homeless youth in this study report high rates of substance use, mental health disorder, and self-medication with substances. Endorsement of self-medication as a motivation for substance use is not contingent on particular types of substances. Youth who report symptoms of PTSD or depression, or report past year suicidal ideation, are much more likely to also report utilizing substances to self-medicate for tension/anxiety, sadness, and to feel better after something bad happened. Conclusions: Effective treatment of mental health disorder/substance use comorbidity will require attention to both issues, and providers should recognize the self-medication interplay between symptoms and substance use. Further longitudinal research is needed to better understand self-medication in this population, and the ways in which it may exacerbate the severity of homelessness experiences.