Many teachers continue to stereotype pupils by gender and treat them differently, often using softer language with girls.
But pupils believe that male and female teachers treat them the same.
A separate study carried out by the research team led by Professor Christine Skelton found that most teachers thought gender influenced the way they worked with children.
It said: "If a study had uncovered these behaviours 10 years ago then it might have been thought that some in-service training using materials from the Equal Opportunities Commission would have been in order. However, the emergence of the boys' underachievement debate provided legitimacy for treating boys differently from girls."
Of the 51 teachers who took part in classroom observations and interviews, two-thirds responded differently to boys and girls.
Many said they used softer language when speaking to girls.
One male teacher, looking at children's handwriting said: "I came to a girl and said 'Oh that's lovely', but I wouldn't have said that to Matthew."
A female teacher described how she would try to get pupils on side by using pet-names.
"I call boys 'darl' as well as the girls. But I don't ever call girls 'mate'. I call the sort of cockier boys 'mate'. Maybe it's me trying to get them on side, because they can be quite cocky and shout a lot."
Male teachers often spent more time on boys and saw them as more needy.
The study found that girls were often ignored when they had their hands up and boys were asked to answer questions instead.