The report, the largest-ever survey of young people's health, showed poverty was the biggest factor affecting the physical and emotional health in children.
It confirmed previous research by the Health Education Authority which had revealed adults from deprived backgrounds had the worst health in the country.
According to the Department of Health report, boys from low-income families were most likely to take up smoking and drinking, to have high blood pressure, suffer obesity and low self-esteem.
"These findings make shock headlines," said chief medical officer Liam Donaldson.
The report, The health of young people 1995-1997, found 40 per cent of teenagers smoked regularly, although the lower social classes and those with smoking parents were most likely to carry on as adults. More than half of all young men aged 18-24 said they drank heavily more than once a week, compared with just over 10 per cent of young women. Boys also tended to have more behavioural problems and had more serious accidents, such as car crashes and sports injuries.
Dr Paola Primatesta, at University College London, said she feared for the future of the nation's manhood. She blamed lax social attitudes for the decline. She said: "Boys are allowed to take more risks. It's considered okay for them to smoke and drink a bit more. Society accepts that boys do these things and somehow it's considered less harmful."
Almost a third of older teenagers are described as overweight, with just under 10 per cent of young men described as obese. A "substantial" proportion of young people regarded themselves as too heavy and a still higher proportion were trying to lose weight. More than a third of young women aged 16-24 said they were heavy and almost half were trying to lose weight. Young women tended to perceive themselves as fat when they were not.
Less than a fifth of children ate fresh vegetables once a day, with less than 10 per cent of those forming the lowest social classes doing so. However, almost a third of all children ate sweet foods and drank soft drinks daily.
Mr Donaldson also called for more children to be encouraged to take up sport. Excluding PE at school, 29 per cent of boys and 44 per cent of girls did not participate in physical activities lasting 30 minutes or more.
lA new sex education programme aimed at cutting Britain's soaring teenage pregnancy rate was launched this week, as it was revealed that the number of pregnant girls under 16 had risen by 11 per cent last year. 'Understanding Contraception', a new education programme from Brook Advisory Centres, the youth sex advice charity, is aimed at 14-year-old girls.