In such schools, there are likely to be dramatic discrepancies between the achievements of girls or boys in examinations, an absence of books that take account of gender issues, and failure to raise pupils' aspirations.
"Merely giving prominence to an equal opportunities policy does not guarantee that both sexes are well provided for," says the report.
The research finds that girls are more successful than boys at every level at GCSE in almost all major subjects, even those traditionally considered "male", such as maths and science. The only exception at GCSE is physics. At A-level, boys score more top and bottom grades than girls.
The report, a "discussion document", provides more questions than answers. It suggests schools should consider why girls seem to conform more willingly to the school culture - being more organised, more conscientious and able to present work well - all of which helps at GCSE. The report asks what schools can do to help boys to acquire these qualities, but also encourages teachers to consider whether they might be overvaluing them - neat, well-managed work can "mislead teachers into thinking girls are making progress".
The researchers are wary of recommending one type of school over another. In the hierarchy, girls' schools tend to do best, mixed schools second and boys' schools third. But, as the report points out, girls' schools are often selective and in advantaged areas.