BACKGROUND: We assessed change between 1996 and 2006 in the opinions of the general public on priorities for the prevention of health problems. METHODS: Postal questionnaire surveys in 1996 and 2006, in representative samples of the general population of Geneva, Switzerland. Participants indicated, for each of 13 health problems, a priority rating for the spending of prevention resources. RESULTS: There were 742 participants in 1996 (response rate 75%) and 1487 in 2006 (response rate 76%). According to participants, in 2006, resources should be spent, with priority, for: the prevention of sexual abuse of children (67% answered 'high priority'), illegal drugs (58%), AIDS (55%), tobacco smoking (45%), road traffic accidents (43%), alcoholism (42%), family violence (42%), suicide in young people (39%), mammography screening for breast cancer (37%), abuse of medications (27%), cannabis use (24%), poor diet (22%) and lack of physical activity (20%). Between 1996 and 2006, the largest change was observed for tobacco smoking (+18.6% answered 'high priority'), poor diet (+11.4%), lack of physical activity (+10.8%) and AIDS (-10.8%, P < 0.001 for all change scores). CONCLUSIONS: Smoking, poor diet and lack of physical activity were more likely to be perceived as priorities in 2006 than in 1996, whereas priority ratings decreased for AIDS. The prevention of sexual abuse of children was perceived as the highest priority by all respondent groups.