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BackgroundNumerous surveys of medicinal plant use among college students abound, but none compare use between students enrolled in two different Universities with significantly different ethnic compositions. The objective of this study is to compare medicinal plant use between two different ethnic college populations and explore differences between student medicinal plant users and non-users for comparison with previous research.MethodsStudents (n = 721) at a large research university (n = 498) and a Pan-Tribal University for Native Americans (n = 233) completed surveys in October 2011 to assess past year medicinal plant use. The Mann-Whitney U test, Chi Square test, and General Linear Model were used to compare demographics and self-reported use of medicinal plants among students at both Universities and between past year users and non-users.ResultsOver 23 % of university students surveyed reported past year medicinal plant use. Users were more likely to use commercial tobacco products and to report poorer health than non-users. While Native American student medicinal plant users reported significantly higher rates of commercial tobacco use, lower self-assessment of health, and less use of prescription medicine than non-Native users, no significant differences in prevalence of medicinal plant use were found between University student populations.ConclusionsResults are consistent with preexisting data showing higher rates of medicinal plant use among college students compared to the larger US population of adults and demonstrate previously documented health disparities in Native American populations compared to non-Native Americans.Electronic supplementary materialThe online version of this article (doi:10.1186/s12906-015-0725-1) contains supplementary material, which is available to authorized users.