BACKGROUND: Data targeting trends in legal and illegal substance use by adolescents are scarce. Using the data from two similar large national surveys run in 1993 and 2002, this paper assesses secular trends in rates of substance use among 16-20-year-old Swiss adolescents. METHODS: Self-reported regular use of tobacco, alcohol misuse, regular cannabis use (01 occasion over last 30 days) and lifetime use of psychoactive medication, LSD, ecstasy, cocaine and heroine were assessed through identical questions using an anonymous self-administered questionnaire. 9268 (1993) and 7428 (2002) high school students and apprentices were included in the analyses. RESULTS: There is a higher proportion of regular smokers among apprentices than among students (p <0.001). Between 1993 and 2002 the increase in regular tobacco consumption was significant among both female and male apprentices (p <0.001) but not among students. Between 1993 and 2002 alcohol misuse significantly increased in all four groups (p <0.001). It is more prevalent among males than among females (p <0.001) and higher among apprentices than among students (p <0.001). Regular use of cannabis has increased in the four groups (p <0.0001). It is higher among males than among females (p <0.001), while it is largely the same among students and apprentices. While the increase in ecstasy use is highly significant in all four groups (p <0.001), the increase in LSD and cocaine use is significant among apprentices only (p <0.001). Use of LSD, ecstasy and cocaine is more prevalent among males than among females (<0.001) and higher among apprentices than among students (p <0.001). CONCLUSION: The secular increase in psychoactive substance use among older Swiss adolescents calls for the implementation of effective strategies both from individual and public health viewpoints.