Scarce data exist on the use of complementary and alternative medicine (CAM) by asylum seekers in Switzerland and their perception of discrimination. A cross-sectional study assessed the prevalence and type of CAM used by asylum seekers in one region of Switzerland and evaluated their self-perceived discrimination. Among the 61 asylum seekers who participated, lifetime prevalence of CAM use was 46%, with 28% reporting its use during the last year. Herbal medicine was the most frequently used CAM. Self-perceived discrimination was reported by 36% of asylum seekers, mainly related to their national origins. CAM users had a tendency to report more discrimination than non-users (44% vs. 30%). CAM use is prevalent among asylum seekers. Considering the importance of herbal medicine use and that only half of the respondents disclosed CAM use to their physician, clinicians should ask about it, notably because of potential risks of herb-drug interaction.