A study of hundreds of youngsters found the risk of a range of mental and physical conditions doubled among those from broken homes.
It is not the divorce itself that is the problem but the way it is handled - with rowing couples causing kids stress, which can trigger disease.
Psychologist Maria Seijo Martinez, of the University of Santiago de Compostela, Galicia, Spain, said: "Poor handling involves very high levels of interparental conflict, which makes it very difficult to maintain a good relationship.
"If children are exposed to these family situations for prolonged periods, they often experience toxic stress."
The findings published in the European Journal of Education and Psychology add to evidence that couples who split up endanger the wellbeing of children - usually their biggest concern.
The researchers found cases of genitourinary and gastrointestinal infections - as well as dermatological and neurological disorders affecting the skin and brain - all rose dramatically.
They said divorce causes psychological and social stress. having a major impact on the physical and emotional health of all members of a family. Other relatives are also sometimes affected.
So Ms Seijo Martinez, a social psychology student at the University of Santiago de Compostela, Galicia, Spain, and colleagues analysed children's health problems related to their exposure to a parental separation.
She said: "It is not the break up in itself that has negative effects on the children's health, but improper handling of the situation by the parents. This is indicated in the scientific literature and validated by our data,"
Experts believe physical, psycho emotional and behavioural issues are linked mainly to inadequate management of the break up.
High levels of conflict, a lack of co parenting or violence within the family increase the risk involved in divorce and its impact on child adjustment.
Ms Seijo Martinez believes this causes an intense, prolonged activation of the body's stress responses, which are the main cause of these physical effects.
Last month a study of 19,000 British children found fighting that goes on during a marriage was more damaging than the split itself.
They were about 30 per cent more likely to have behaviour issues because of the arguing at home they had witnessed.
Previous research has shown children of divorce are more likely to get divorced themselves in the future.
Particularly in acrimonious cases, when the atmosphere is poisoned by arguments, enmity or even violence, children are likely to end up doing badly at school.
Their behaviour often deteriorates and, according to statistics, they're more likely to grow up to become risk-taking teenagers and even anti-social adults.
Not only that, but the broken relationship between their parents may make it very hard for these children to form secure and trusting relationships later on.
The number of divorces in England and Wales in 2013 was 114,720, involving 94,864 children under 16.
Among these children, 21 per cent were under 5 and 64 per cent were under 11 years old.