The scientists said the findings, part of ongoing work in a larger "Children of the 90s" study, could indicate that exposure to tobacco smoke before the start of puberty in men may lead to metabolic changes in the next generation.
"This discovery of transgenerational effects has big implications for research into the current rise in obesity and the evaluation of preventative measures," said Marcus Pembrey, a professor of genetics at University College London, who led the study and presented its findings at a briefing on Wednesday.
Smoking rates in Britain and some other parts of Europe are on the decline, but worldwide, almost one billion men smoke - about 35 percent of men in developed countries and 50 percent in developing ones, according to the World Health Organization.
While previous studies in animals and in people have found some transgenerational health impacts, the evidence so far is limited. It points, however, to epigenetics - a process where lifestyle and environmental factors can turn certain genes on or off - having an effect on the health of descendants.
Pembrey said his team's research was prompted in part by signals from earlier Swedish studies that linked how plentiful a paternal ancestor's food supply was in mid childhood with future death rates in grandchildren.
For the new study, published in the European Journal of Human Genetics, the researchers had access to detailed lifestyle, genetic and other health data from 9,886 fathers.
Of these, 5,376, or 54 percent, were smokers at some time and of those, 166, or 3 percent, said they had started smoking regularly before the age of 11.
Looking at the next generation, the team found that at age 13, 15 and 17, the sons of men who started smoking before 11 had the highest Body Mass Index (BMI) scores compared with the sons of men who had started smoking later or who had never smoked.
"These boys had markedly higher levels of fat mass - ranging from an extra five kilograms (kg) to 10kg between ages 13 and 17," the study said.
Although it was there, the effect was not seen to the same degree in daughters.
Image: Young man smoking, via Shutterstock