The shorter you are, the greater your risk of heart problems, a team at the University of Leicester says.
The study, of nearly 200,000 people, found sections of DNA that control both height and heart health.
The findings, published in the New England Journal of Medicine, showed every extra 2.5in (6.4cm) cut coronary disease incidence by 13.5%
The British Heart Foundation said short people should not be unduly worried and everyone needed a healthy lifestyle.
Coronary heart disease, which includes heart attacks and heart failure, is the leading cause of death in the UK.
More than 73,000 people die from the disease each year.
'Small' risk
The idea that height plays a role in heart health was first proposed more than 50 years ago, but researchers did not know why.
Some thought the relationship was a consequence of other factors, such as poor childhood nutrition stunting height and also affecting the heart.
But the study at the University of Leicester suggests the answer lies deeper - inside our DNA.
They analysed 180 genes that have a known link to height.
The results showed that every 2.5in of height affected the risk by 13.5%, so the difference in heart risk between a five-footer and a six-footer would be around 64%.
Professor Sir Nilesh Samani, from the University of Leicester, told the BBC News website: "In the context of major risk factors this is small - smoking increases the risk by 200-300% - but it is not trivial.
"I wouldn't say shorter people need to take greater precautions, because if you're 6ft 1in (1.85m) you still need to stop smoking.
"This is only one of many factors affecting risk, everybody should be cautious."
Genetic clues
The study also showed those genes cutting height were also increasing the amount of cholesterol and fats in the bloodstream.
The researchers believe some of the height genes may also be controlling both growth and blood vessel development.
"Understanding these pathways may lead to new treatments and that may be more valuable in the longer term," Prof Samani added.
But it is worth remembering it is not all good news being tall. as height increases the risk of cancer.
Prof Peter Weissberg, the medical director at the British Heart Foundation, said: "This study does not suggest that short people should be unduly worried about their health or that doctors need to focus on the health of shorter patients.
"Everyone, regardless of their height, should do everything in their power to reduce their risk of future heart disease by eating a healthy diet, exercising regularly and not smoking.
"Currently available health checks are designed to help you understand what measures you need to take to reduce your personal risk."
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