Boys who are disengaged with school tend to behave poorly and become disruptive. For disaffected girls it leads to high levels of absence, with 41 per cent of lessons being missed, Ofsted said.
The findings come in a study into how schools can re-engage pupils who have become disruptive, are given temporary exclusions or miss more than 20 per cent of school.
Schools are having to battle the attractions that pupils see in gangs, criminal activity and drug-taking, the report said.
Another common problem facing schools is parents who refuse to co-operate with teachers and, in some cases, collude with pupils against the school.
Inspectors visited 29 secondary schools between September 2007 and February this year that had a good track record in reversing absentee rates. Successful schools offered courses in anger management, team building, personal safety and sexual health to reach out to pupils in danger of dropping out, inspectors said.
They also had to reach out to children as young as 10, in their final year of primary school, who were already displaying aggressive behaviour. Secondary school staff built relationships with these pupils to ease the transition.
The report follows the launch of a consultation last week into pupil wellbeing indicators, which schools could be judged on from September 2009. The proposed indicators include data already available, such as a school's overall attendance record and the take-up of school lunches.
The measures being suggested also include asking pupils and parents about how the well the school promotes wellbeing - for example, whether the school encourages physical exercise and deals effectively with bullying.