Women who take the Pill each day have a key brain region which is smaller, experts have found for the first time.
The hypothalamus is crucial for the normal production of hormones and plays a role in mood, appetite, sex drive and sleep.
Researchers at Montefiore Medical Center in New York City scanned the brains of 50 women to make the conclusion.
They saw a 'dramatic difference' in the size of the hypothalamus in women who took birth control pills.
But they said cognitive performance or behaviour did not change - despite the brain region being around six per cent smaller.
However, other preliminary evidence from the same team found a link between the smaller size and anger and depressive symptoms.
The research will be presented at the Radiological Society of North America's annual meeting. It is not yet published in an academic journal.
Women who take the Pill every day have a smaller brain region called the hypothalamus, involved in hormone regulation, scientists find for the first time
Fifty women underwent brain MRIs to look at the size of their hypothalamus (in red)
Lead author Dr Michael Lipton, said: 'There is a lack of research on the effects of oral contraceptives on this small but essential part of the living human brain.'
He added that his team can confirm, 'for the first time', using the Pill is linked with a 'smaller hypothalamic volume'.
The study recruited 50 healthy women, including 21 taking oral contraceptives and had never had brain injury or mental illness. All underwent brain MRIs.
The hypothalamus in women on birth control were about six per cent smaller than those of other women, Discover reports.
'We found a dramatic difference in the size of the brain structures between women who were taking oral contraceptives and those who were not,' Dr Lipton said.
He told Discover: 'I like to tell people that for all parts of the body, size matters most in the brain.' But he added: 'It may not represent a risk at all.'
Other findings from the study, which Dr Lipton described as 'preliminary', were that smaller hypothalamic volume was linked with greater anger.
There was also a strong correlation between the size of hypothalamic volume and depressive symptoms.
But Dr Lipton found no significant correlation between hypothalamic volume and cognitive performance. It is not clear how this was studied.
The hypothalamus is located at the base of the brain above the pituitary gland and helps regulate bodily functions which are essential for survival.
Disease of the hypothalamus, most often caused by brain injury,