Researchers from University La Sapienza in Italy looked at hormone levels in 25 men and 35 women with MS, and in 36 people without the disease.
Women with low testosterone levels were found to have more brain tissue damage. There was no difference in testosterone levels between men with or without MS.
The Journal of Neurology, Neurosurgery and Psychiatry published the study.
It is known that MS affects twice as many women as men, and that it is significantly less active during pregnancy, suggesting hormones do play a role in its development.
MS is an inflammatory disease which causes a range of symptoms from fatigue and numbness to difficulties with movement, speech and memory.
The relapsing-remitting form of the disease follows a characteristic pattern of periods of deterioration followed by partial recovery.
Brain scans
In this study, researchers compared levels of a range of hormones in the healthy people and those with MS.
The average age of the participants was 32, and those with MS had had the relapsing-remitting form of the disease for an average of six years.
Women were tested during both phases of their menstrual cycle, to account for variations in hormone levels. None used oral contraceptives, and all had normal cycles.
Men and women with MS were also given magnetic resonance imaging (MRI) brain scans to identify areas of tissue damage and inflammation, caused by the disease.
It was found that women with MS had lower levels of the male hormone testosterone throughout their monthly cycle compared to women who did not have the condition.
The MS group also had more of the lesions which are caused by inflammation in the relapse period of the disease.
There were some women within the MS group who had relatively high levels of testosterone.
These women were more likely to show signs of the irreversible tissue damage, linked with disability, which is more likely to be seen in the remitting stage of the disease where tissue is not inflamed.
There was no difference in testosterone levels between men with MS and men who did not have the condition.
However, men with MS who had the highest levels of the female hormone oestradiol were found to have the greatest degree of brain tissue damage.
None of the other hormones studied seemed to have any impact on the findings.
'Important step'
Writing in the Journal of Neurology Neurosurgery and Psychiatry the team, led by Dr Carlo Pozzilli of the Department of Neurological Sciences at University La Sapienza: "We propose that oestrogens and testosterone play a role in modulating the development of brain tissue damage in MS.
"The respective contribution of these two hormones and their types of actions and interactions deserve further analysis."
Chris Jones, chief executive of the MS Trust, said: "It's one of the conundrums of MS that in pregnant women with MS where oestrogen levels are high, there is a significant reduction in relapses, yet raising oestrogen levels in non-pregnant women has no effect on relapse rate.
"There is also little understanding of why twice as many women as men develop MS, yet their disease tends to be less aggressive.
"This research on abnormal testosterone levels in women with MS and those men with MS with higher oestradiol levels, showing correlation between disability and tissue damage on MRI, therefore seems to be another important step in resolving this conundrum."
Mike O'Donovan, head of the MS Society, added: "This new research tells us more about the role hormones play in this complex condition and certainly requires further investigation."