The birth defect is known as hypospadias, where the opening of the urethra is on the underside of the penis instead of the tip. It affects roughly one in 200 newborn boys.
No one is sure what causes hypospadias, though there does seem to be a genetic component. And some studies have found that the risk is higher when moms are older than 35 or obese before pregnancy.
In theory, organic food choices could be related, according to the researchers of the new study, led by Jeppe Schultz Christensen of Rigshospitalet in Copenhagen, Denmark.
That's because organic foods should have less pesticide residue than conventional foods. And certain pesticides contain so-called endocrine-disrupting chemicals - meaning they can have effects on reproductive hormones.
But in their study, the researchers found that overall, organic food choices were not linked to hypospadias risk.
The one exception was that a high intake of non-organic butter and cheese was related to an increased risk. But experts say that does not necessarily equal cause-and-effect.
"I'd be very cautious in interpreting these results," said Suzan Carmichael, an associate professor of pediatrics at Stanford University School of Medicine in California.
Carmichael was not involved in the new research, but has studied potential environmental risk factors for hypospadias and other birth defects.
It's not clear what to make of the connection between high consumption of certain non-organic dairy foods and hypospadias, according to Carmichael. There could be other things about moms' lifestyles or health at work.
"I think the main finding is that most non-organic foods were not associated with the risk," Carmichael said.
The findings, reported in the Journal of Urology, are based on interviews with 306 moms whose sons were born with hypospadias and 306 who had healthy baby boys. The women reported on how often they chose the "organic alternative" for different food groups during pregnancy.
Then they were asked about their current eating habits: how often they ate eggs, cheese, fruits and vegetables and meat. The researchers used that as a "proxy" for how often the moms ate those foods during pregnancy.
Overall, moms who'd chosen organic during pregnancy were no less likely to have a boy with hypospadias than moms who'd eaten conventional foods.
The one exception was seen with moms who currently ate both butter and cheese at least once a day, and who'd "rarely or never" eaten organic during pregnancy. They were twice as likely to have a baby with hypospadias, versus women who had little butter and cheese, and had gone organic at least sometimes while pregnant.
That hints at a possible role for pesticide contaminants in fatty dairy foods, according to the researchers.
On the other hand, that might not be the explanation at all.
"I think that the organic choice is probably related to general healthy lifestyle and behaviour, and that may be an explanation to the findings," Tina Kold Jensen, one of the researchers on the study, said in an email.
"This really doesn't add evidence on whether women should choose organic," Carmichael said.
She added, though, that the findings don't mean a possible link should be dismissed.
There is lab research suggesting that endocrine disrupting chemicals could contribute to hypospadias. Studying a possible connection in humans is a lot more complex, however, Carmichael pointed out.
Singling out any one environmental exposure as a culprit in birth defect risk is always difficult.
The strongest kind of study would follow a large group of pregnant women, get detailed information on different exposures and, ideally, do blood tests to see what a woman's actual exposure to a given chemical was.
Those are tough studies to do, in part because hypospadias is fairly uncommon. So you'd have to recruit and follow a large number of women, Carmichael pointed out.
"It's really important to ask these questions," she said, "But it's also challenging."
The US Centers for Disease Control and Prevention is currently running a large study on the potential risk factors for various birth defects, including hypospadias. birth defects, including hypospadias.