Objectives To investigate sexual behaviour and contraceptive use among first-year high school students in two Swedish cities in 2009, to compare male and female students, students in theoretical and vocational study programmes, and their sexual behaviour with that reported in 1979, 1989 and 1999. Methods In a cluster sample of 20 classes, students (N = 387), median age 16 years, completed a questionnaire consisting of 46 questions. Results More girls than boys had experienced petting (p <= 0.003) and had received oral sex (p <= 0.01). More boys than girls had masturbated (p <= 0.0001) and watched pornography (p <= 0.0001). The median age at first sexual intercourse was 15 years. Students in vocational programmes were more sexually experienced compared to their theoretical peers. The proportion of students having had sexual intercourse (p <= 0.0002), and contraceptive use at first (p <= 0.0001) and latest (p <= 0.0001) sexual intercourse increased from 1979 to 2009. Alcohol use at first intercourse decreased over the period (p <= 0.0001). Conclusions Girls were more sexually experienced than boys, as were students in vocational programmes compared to their theoretical peers; this should be considered when tailoring sex education and counselling. Over time, an increase in students having had sexual intercourse, and contraceptive use at first and latest sexual intercourse was found.