More than 140,000 children aged 12 to 15 were surveyed.
In 2001, fewer respondents thought HIV could be passed on by sharing needles or by having sex without a condom, compared to the same age group in 1995. The best knowledge was in 14- to 15-year-old girls.
Dr David Regis, director and research manager of the Schools Health Education Unit, said: "There is a level of concern about HIV and Aids that was around before that is not here now."
He said that youngsters' anxiety and the emphasis given in schools was an issue.
Regis added that sex education was focusing on infections such as chlamydia and herpes because they were more common.
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