Men who are under 5ft 3in (1.63 metres) are twice as likely to suffer a particular form of stroke, known as haemorrhagic, as those over 5ft 7in (1.75m).
A four-inch (10cm) height advantage equates to a 20% lower risk of suffering all kinds of stroke, according to research funded by the Stroke Association and Chest, Heart and Stroke Scotland.
Around 100,000 people a year in the UK suffer a first stroke and it is the biggest cause of disability.
Of the stroke victims in the study, 23% were classified as ischaemic - meaning the blood supply to the brain is cut off and causes damage.
A further 8.8% were classed as haemorrhagic, meaning the stroke was caused by bleeding in or around the brain, and others were not defined.
Women under 5ft 0in (1.52m) face a 30% higher risk of a haemorrhagic stroke.
There was little difference in the risks of ischaemic strokes based on height, the report found.
Embryonic development link
The study, published in the Journal of Epidemiology and Community Health, compared the people who did not suffer a stroke with the 1,027 who did fall victim to the condition.
More than 15,000 people in the west of Scotland were followed for 20 years from 1972 by a team from Bristol and Glasgow Universities.
Report author Dr Peter McCarron said: "Our findings add to the evidence that early life factors may determine risk of stroke."
It is thought the stroke/height association dates back to a baby's development in the womb.
Scientists believe reduced growth seems to result in a greater flow of blood supply and nutrition to the baby's body and not the brain, which may permanently alter the brain's structure and make it more susceptible to stroke later in life.
Eoin Redahan of the Stroke Association said: "This study backs up previous research on the link between height and stroke.
"However, the reasons are not clear - as adults there are some risk factors for stroke that we can control such as high blood pressure, poor diet and lack of exercise.
"Whereas our height - which may be influenced by foetal or childhood growth - has already been fixed."