Background: As part of the independent evaluation of Healthy Respect (a national demonstration project to improve teenage sexual health in Scotland) this study examined the effect of the school-based sexual health education intervention comprising multiprofessional classroom delivery and alongside drop-in clinics on teenage sexual behaviour outcomes. Methods: Before-and-after cross-sectional surveys of secondary school pupils (average age 14 years and 6 months) were used in 10 Healthy Respect intervention schools in Lothian region and 5 comparison schools without intervention in Grampian region (2001 and 2003). Results: By 2003, the proportion of pupils in Lothian feeling confident about getting condoms and using condoms properly significantly increased, more Lothian pupils (particularly boys) showed improved knowledge about condoms being protective against sexually transmitted infections. No further evidence of improved knowledge, attitudes, or intentions was evident after the intervention. Pupils in Lothian remained more likely to think using a condom would be embarrassing (especially girls), would reduce sexual enjoyment (especially boys), and intentions about condom use (as closer predictors of actual behaviour change) showed no significant improvement. More Lothian (24%) than Grampian (19%) pupils report having had sexual intercourse at age <16 years, both before and after the intervention, with no evidence of a significant reduction in Lothian by 2003. Overall differences in attitudes to condom use by gender were noted. Findings remain consistent in both unadjusted and adjusted comparisons. Conclusion: These findings demonstrate limited impact on sexual health behaviour outcomes, and raise questions about the likely and achievable sexual health gains for teenagers from school-based interventions.