New research has suggested boys are 14 times more likely to be struck down with a rare heart complication called myocarditis.
The data, from the US, will likely fuel an already fierce debate over Britain's decision to press ahead with inoculating all 16 and 17-year-olds.
Last week, the Government's advisory panel ruled older teenagers should be given their first dose. Ministers plan to invite them before they head back to schools and colleges in September.
But health officials have yet to make concrete plans for children to get top-ups. They want to wait for more safety data about myocarditis before pressing ahead.
Real-world data from the US, which has been vaccinating children for months, have shown teenage boys to be at a higher risk.
It prompted one member of the Joint Committee on Vaccination and Immunisation, which green-lighted the move to jab children, to admit different advice for boys was 'theoretically on the cards'.
There is already precedent for just giving vaccinating just one gender, with the HPV jab offered only to girls until 2018.
The findings echo data from the Centers for Disease Control and Prevention (CDC), which suggests the risk is up to nine times higher among teenage boys.
All 15 experienced chest pain, which started a couple of days after being vaccinated and lasted for up to nine days.
None were struck down with a serious bout of myocarditis or required intensive care. All were discharged within five days.
But doctors at Boston Children's Hospital cautioned that the long-term risks of post-vaccination myocarditis 'remain unknown'.
Myocarditis — inflammation of the heart muscle — is usually triggered by a virus. In most cases, the illness goes away and there are no complications.
But in rare cases, there can be damage to the heart which can stop the organ from pumping properly. Some patients may need a heart transplant.
Within two weeks, most of the children studied no longer experienced inflammation symptoms.
Lead researcher Audrey Dionne said the reduced symptoms aligned with measurements that doctors took of patients' hearts.
Troponin, a protein used to detect heart injury, was higher in all of the children when they arrived at the hospital. But it approached normal levels by the time they were discharged.
Readings of patients' left ventricles also suggested the teenagers' hearts returned to normal after a few days of symptoms.
The doctors noted the pattern was distinct from other forms of heart inflammation caused by severe heart disease. In those cases, patients are more likely to require intensive care and have a higher risk of dying.
Overall, this study suggests that post-vaccine inflammation — while a severe side effect for teen boys — is a much lower risk than getting Covid.
But larger and longer term studies will be needed to inform policy on vaccinating younger groups.
The UK's decision last week to offer 16 and 17-year-olds the jab promoted backlash among top experts who claimed it was unethical.
Today, Professor Robert Dingwall, a professor of sociology at Nottingham Trent University and former Government adviser, told MailOnline: 'The myocarditis risk does seem to be higher in boys but these are very small numbers to shape a policy around.
'If anything, it supports the JCVI position of waiting to see what emerges from the US before making any wider recommendations for UK children.'
Professor Helen Bedford, an expert in children's health at University College London Great Ormond Street Institute of Child Health, warned against jabbing children.
She told MailOnline: 'The real issue here is whether we should be vaccinating children at all.
'Children are at very small risk of Covid so the question is who would benefit if they are vaccinated?
'We already have very high vaccine uptake among adults, much higher than the US and Canada.
'Meanwhile, large parts of the world have no access to vaccine at all, even for health care workers, but are at much greater risk from disease.
'Without vaccination, the infection will continue to circulate with the real possibility of emergence of variants which may evade current vaccines and then impact even on highly vaccinated populations.
'This is a global issue and I think there is a strong case for the UK to set an example by giving vaccine to other countries before boosting adults or vaccinating children here.'
The patients arrived at the hospital with elevated troponin levels, an indicator of heart injury - but their hearts recovered significantly during short hospital stays
'But vaccine escape is inevitable and I think that adds to the argument not to blanket vaccinate children aged 12 to 15.
'I don't think that is going to help you minimise that when the risk of transmission is there.
'With kids, they're not going to stop transmission, they're not going to stop escape variants nothing is so actually it's all about the risk to the child themselves.
Comment: Vaccines don't really do all that much to stop variants nor transmissions in any age group.
'So yes we should offer it to vulnerable children but I don't think that currently, the way it stands, vaccine roll-out to all of them is the way forward.'
Professor Paul Hunter, an infectious disease expert at the University of East Anglia, told the APPG up to 90 per cent of 17-year-olds already have Covid antibodies.
It suggests they had previously been infected, or currently had the virus and were developing antibodies.
Regarding the roll-out to 17 year olds, Professor Hunter said: 'My concerns are why are we vaccinating an age group that has already been infected and recovered.
'Is it necessary? Do we know enough about potential side effects in teenagers that have already been infected?'
But other experts were in favour of giving the jab to teens, with scientists saying jabbing children is key to curbing the spread of the virus and minimise the numbers having to take days off school to self-isolate.
Others say it will be impossible to achieve any kind of population immunity without inoculating under-18s.
Professor Lawrence Young, an infectious diseases expert at Warwick Medical School, told MailOnline told the risk of getting myocarditis is 'much higher' from Covid itself compared to the risk from vaccination.
He said: 'Estimates vary, but a recent study from the US estimated that covid causes around 450 cases of myocarditis per million males aged between 12 to 17 and 213 cases per million in females aged 12 to 17.
'This compares with a risk following mRNA vaccination of 76.5 cases per million in males in data from the US and Israel.
'So the overall risk of myocarditis is decreased by being vaccinated.
'The bottom line is that myocarditis is a rare side effect, usually very mild and manageable, and certainly preferable to both the acute and long-term consequences Covid itself.'
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