There is no firm evidence of this in humans, but Washington State University research showed a clear effect in rats.
They isolated defects linked to kidney and ovary disease and even obesity.
The work implicates a class of chemicals found in certain plastics, as well as one found in jet fuel.
The idea of "epigenetics" - that parents do not just pass their genes to their children, but subtle differences in the way those genes operate - is one of the fastest growing areas of scientific study.
The work of Dr Michael Skinner centres around the effects that certain chemicals can have on these processes, if the female is exposed at key points during pregnancy.
So far they have documented measureable effects from a host of environmental pollutants including pesticides, fungicides, dioxins and hydrocarbons.
However, they stress that the results are not directly transferable to humans yet, as the levels of chemicals used on the rats were many times more concentrated than anything a person would experience in normal life.
There is no data on even how an animal would respond at different doses, and no clues as to how the chemicals are causing these changes.
The studies, published in the journals PLoS One and Reproductive Toxicology, looked at the impact of phthalates, chemicals found in some forms of plastics, and a substance called JP8, found in jet fuel.
Rats exposed to phthalates had offspring with higher rates of kidney and prostate disease, and their great-grandchildren had more disease of the testicles, ovaries and obesity.
Female rats exposed to the hydrocarbon JP8 at the point in pregnancy when their male foetuses were developing gonads had babies with more prostate and kidney abnormalities, and their great-grandchildren had reproductive anomalies, polycystic ovary disease and obesity.
Dr Skinner said: "Your great-grandmother's exposures during pregnancy may cause disease in you, while you had no exposure.
"This is a non-genetic form of inheritance not involving DNA sequence, but environmental impacts on DNA chemical modifications.
"This is the first study to show the epigenetic transgenerational inheritance of disease such as obesity."
Andreas Kortenkamp, professor of human toxicology at Brunel University, said the results were "potentially very interesting", but much more work would need to be carried out before any impact on humans could be considered.
He said: "This is an exploratory study, but the authors themselves are clear that the data do not allow the possible risk to people to be assessed."
"There is a currently a lack of information about the dose-response relationship, and at this stage we are very unsure about the mechanisms that are involved."