Differences in children's exam results at secondary school owe more to genetics than teachers, schools or the family environment, according to a study published yesterday.

The research drew on the exam scores of more than 11,000 16-year-olds who sat GCSEs at the end of their secondary school education. In the compulsory core subjects of English, maths and science, genetics accounted for on average 58% of the differences in scores that children achieved.

Grades in the sciences, such as physics, biology and chemistry, were more heritable than those in humanities subjects, such as art and music, at 58% and 42% respectively.

The findings do not mean that children's performance at school is determined by their genes, or that schools and the child's environment have no influence. The overall effect of a child's environment – including their home and school life – accounted for 36% of the variation seen in students' exam scores across all subjects, the study found.

"The question we are asking is why do children differ in their GCSE scores? People immediately think it's schools. But if schools accounted for all the variance, then children in one classroom would all be the same," said Robert Plomin, an expert in behavioural genetics who led the study at King's College London.

To tease out the genetic contribution to children's school grades, the researchers studied GCSE scores of identical twins (who share 100% of their genes) and non-identical twins (who share on average half of the genes that normally vary between people). Both groups share their environments to a similar extent.

Comparing the twins' exam scores allowed the scientists to work out how much of the variation was down to genetics, and how much to environment. For example, when identical twins get different GCSE scores, the cause cannot be genetic, so it must be what scientists call "non-shared environment" effects – such as the better student having a better teacher.

A child's performance is influenced, but not set, by their DNA. While one child may excel, their identical twin may not. But taking an average over the population studied, around half of the variation in GCSE scores was due to genetics, Plomin found. Details of the study appear in the journal, Plos One.

Writing in the journal, the authors point out that genetics emerges as such a strong influence on exam scores because the schooling system aims to give all children the same education. The more school and other factors are made equal, the more genetic differences come to the fore in children's performance. The same situation would happen if everyone had a healthy diet: differences in bodyweight would be more down to genetic variation, instead of being dominated by lifestyle.

Plomin said one message from the study was that differences in children's performance were not merely down to effort. "Some children find it easier to learn than others do, and I think it's appetite as much as aptitude," he said. "There is a motivation, maybe because you like to do what you are good at."

Genetics, he said, caused people to create, select and modify their environment, and so nature drives nurture, which in turn reinforces nature. A child with a gift for maths seeks friends who like maths. A child who learns to read easily might join a book club, and work through books on the shelves at home.

Michael Reiss, professor of science education at the Institute of Education in London, said that while genetics undoubtedly plays a role in educational performance, the information might not be very useful. "Some people have to wear glasses because of genetic defects, and other people wear them for reasons that have nothing to do with genetics. As long as you are wearing glasses in school, it doesn't matter at all. The genetics is utterly irrelevant," he said.

In the past 10 years, programmes have been developed that help children who have fallen behind with their reading to catch up. The programme does not rely on genetics, but focuses on the particular problems the children have in reading. "It doesn't matter if you're teaching maths, rowing or the trombone. A good teacher is very sensitive to the individual needs of the learner, and I don't think the genetics is going to help very much with that," Reiss said.

Plomin said that educational performance could be affected by thousands of genes, each of which has a minuscule effect. Finding them will be tough, but would allow scientists to work out which gene variants affect performance in different subject areas.

That might produce problems of its own though. "The worry is that parents, teachers and children themselves start thinking 'It's not worth my while trying, I don't have the genes for it', but that's false logic. The big problem is equating genetics with determinism. It's a very powerful [misconception] and difficult to shift," said Reiss.

Plomin believes that education might be improved by enlarging schools so they have enough resources to offer children a greater range of subjects and activities, so each can find out what they are good at.

"Education is still focused on a one-size-fits-all approach and if genetics tells us anything it's that children are different in how easily they learn and what they like to learn. Forcing them into this one academic approach is going to make some children confront failure a lot and it doesn't seem a wise approach. It ought to be more personalised," he said.

"These things are as heritable as anything in behaviour, and yet when you look in education or in educational textbooks for teachers there is nothing on genetics. It cannot be right that there's this complete disconnect between what we know and what we do."