The work by Wellcome Trust Sanger Institute, and partially funded by the British Heart Foundation, sought to discover more about the genetic background of CHD.
Emma Wild was one of those who took part. She and her daughter Emily both have the same form of CHD, though Emily's is more severe. Emma says "information can only help".
CHD affects 1% of people worldwide and around 1.35 million babies each year. It causes problems such as holes in the heart which can need corrective surgery.
The international research, published in Nature Genetics, analysed the protein-coding segments of the genome of 1,900 CHD patients and their parents.
It had previously been thought that many cases might be caused by new genetic mutations which were absent in the parents.
This study found children can instead inherit rare gene variants and it paves the way for affected families to be given clearer advice.
Emma and Emily, who both have a kind of CHD called Tetralogy of Fallot, were part of the research.
Scientists did not find a genetic explanation for their situation, but Emma is still pleased to have been involved.
"They've not definitely found a link between me and my daughter but what they have found is the tip of the iceberg and they can now look into it further," she said.
Emma had to have an operation at the age of two, but had no further effects. When she was pregnant with her daughter Emily, scans showed the baby had the same condition.
"I just thought 'she'll have the same operation as me'. But when she was born, initially they thought there wasn't anything they could do. And now we're celebrating her third birthday.
"I love her dearly and I wouldn't change her. But now I know the information - and possibly even before - I wouldn't have any more children."
Emma, 30, from Grantham in Lincolnshire, said: "We're never going to be able to fix her. We just want to give her as good a quality of life as we can."
Emily has to be fed through a gastrostomy, a tube into her stomach, and sometimes needs oxygen. And she is expected to have a limited life expectancy.
Her mum said: "If I can get her into her 20s, I will have done a really good job."
Prof Jeremy Pearson, associate medical director at the BHF, said: "Here, research has shown for the first time that congenital heart defects are often a question of genetic inheritance.
"In the future, as a direct result of this research, doctors may be able to offer much clearer advice to families where one member has congenital heart disease."