Researchers led by Sarah Kimmins at McGill University in Montreal, Canada, looked at what happened when male lab mice had a diet that was poor in vitamin B9.
B9, also called folate, is present in green leafy vegetables, cereals, fruit and meat.
Women often take folic acid supplements, before and during pregnancy, to reduce the risk of miscarriage and birth defects in their offspring.
But Kimmins' team were startled to find that male mice that had a B9-deficient diet also fathered mice with a higher rate of birth defects, compared to counterparts which had eaten sufficient folate.
"We were very surprised to see that there was an almost 30-percent increase in birth defects in the litters sired by fathers whose levels of folates were insufficient," said one of the team, Romain Lambrot.
"We saw some pretty severe skeletal abnormalities that included both cranio-facial and spinal deformities."
The problem, according to the investigators, lies in the sperm's epigenome, or the "switches" that turn genes -- the protein-making codes for life -- on and off.
This switchgear, influenced by diet or other life experiences, deregulates key genes during the embryo's development, according to their theory.
If the findings in rodents also turn out to hold true for humans, there are important implications for men's diet, said Kimmins.
"Despite the fact that folic acid is now added to a variety of foods, fathers who are eating high-fat, fast-food diets or who are obese may not be able to use or metabolise folate in the same way as those with adequate levels of the vitamin," she said.
"Our research suggests that fathers need to think about what they put in their mouths, what they smoke and what they drink and remember they are caretakers of generations to come."
The study appears in the journal Nature Communications.