The damage – thickening of blood vessel walls – increases the risk of heart attacks and strokes in later life, they say in the European Heart Journal.
In their study of more than 2,000 children aged three to 18, the harm occurred if both parents smoked.
Experts say there is no “safe” level of exposure to second-hand smoke.
The research, carried out in Finland and Australia, appears to reveal the physical effects of growing up in a smoke-filled home – although it is impossible to rule out other potentially contributory factors entirely.
Ultrasound scans showed how children whose parents both smoked developed changes in the wall of a main artery that runs up the neck to the head.
While the differences in carotid intima-media thickness were modest, they were significant and detectable some 20 years later when children had reached adulthood, say the investigators.
Study author Dr Seana Gall, from the University of Tasmania, said: “Our study shows that exposure to passive smoke in childhood causes a direct and irreversible damage to the structure of the arteries.
“Parents, or even those thinking about becoming parents, should quit smoking. This will not only restore their own health but also protect the health of their children into the future.”
The results took account of other factors that might otherwise explain the association, such as whether the children went on to be smokers themselves, but the findings remained unchanged.
However, if only one parent smoked the effect was not seen – possibly because exposure was not as high.
Dr Gall said: “We can speculate that the smoking behaviour of someone in a house with a single adult smoking is different. For example, the parent that smokes might do so outside away from the family, therefore reducing the level of passive smoking. However, as we don’t have this type of data, this is only a hypothesis.”
Regardless, experts say all children should be protected from second-hand smoke.
Doireann Maddock, senior cardiac nurse at the British Heart Foundation, said: “The negative health effects of passive smoking are well known, but this study goes a step further and shows it can cause potentially irreversible damage to children’s arteries increasing their risk of heart problems in later life.
“If you’re a smoker, the single most effective way of reducing your child’s exposure to passive smoke is for you to quit.
“If this isn’t possible, having a smoke-free home and car offers the best alternative to help protect your child from the harmful effects of passive smoke.”
Simon Clark, director of the smokers’ group Forest, said: “We must avoid scaremongering because damage to arteries could be caused by a number of factors including poor diet and other forms of air pollution.
“While it’s sensible and considerate not to smoke around children in a small confined space it’s far too easy to point the finger at smokers when the issue is extremely complicated.”