Their study of nearly 37,000 people, published in the online journal BMJ Open, said balding men were 32% more likely to have coronary heart disease.
However, the researchers said the risks were less than for smoking or obesity.
The British Heart Foundation said men should focus on their waistline, not their hairline.
A shifting hairline is a fact of life for many men. Half have thinning hair by their 50s and 80% have some hair loss by the age of 70.
Researchers at the University of Tokyo sifted through years of previous research into links between hair loss and heart problems.
It's more important to pay attention to your waistline than your hairline”Doireann MaddockBritish Heart Foundation
They showed that hair that went thin on the crown was associated with coronary heart disease. This was after adjusting for other risk factors such as age and family history.
However, a receding hairline did not seem to affect the risk.Focus on lifestyle
Dr Tomohide Yamada, of the University of Tokyo, told the BBC: "We found a significant, though modest, link between baldness, at least on the top of the head, and risk for coronary heart disease.
"We thought this is a link, but not as strong as many other known links such as smoking, obesity, cholesterol levels and blood pressure."
He said younger men losing hair on the top of their head should focus on improving their lifestyle to ensure they keep their heart healthy.
However, he said there was not enough evidence to suggest screening bald men for heart problems.
Coronary heart disease is the biggest killer in the UK.
One in five men and one in eight women dies of the disease.
It is caused by blood vessels that nourish the heart becoming blocked.
Any explanation for the link is uncertain.
There are ideas about increased sensitivity to male hormones, insulin resistance and inflammation in blood vessels affecting both the heart and the hair.
Doireann Maddock, a cardiac nurse with the British Heart Foundation, said: "Although these findings are interesting, men who've lost their hair should not be alarmed by this analysis.
"Much more research is needed to confirm any link between male pattern baldness and an increased risk of coronary heart disease. In the meantime, it's more important to pay attention to your waistline than your hairline.
"Hereditary hair loss may be out of your control, but many of the risk factors for coronary heart disease are not. Stopping smoking, maintaining a healthy weight and being as active as possible are all things that you can do to help protect your heart."
Patrick Wolfe, a professor of statistics at University College London, said: "Right now the link that is seemingly responsible for this relative risk increase is not well understood, and so in future we might look forward to a day when understanding more about the various mechanisms underlying heart disease will tell us more about those underlying male pattern baldness, and vice versa.
"In the meantime it's a case of focusing on the things that we can control - our diet, exercise regimens and other risk factors - to lower our overall risk for heart disease."
