The largest study of its kind has shown the Pfizer-BioNTech Covid-19 vaccine causes far fewer problems than the virus itself in children and young people, after concerns the jab may cause harm.
The risks after being infected with the virus "lasted much longer" compared with post-vaccination, researchers said.
During the pandemic, a link emerged between the Covid-19 vaccine and an increased risk of myocarditis, inflammation of the heart muscle, and pericarditis, inflammation of the lining around the heart.
Most patients who developed symptoms did so within a week of the jab, with cases more common in young males under the age of 25.
The new study, led byexperts at UCL and the universities of Cambridge and Edinburgh, with support from the BHF Data Science Centre at Health Data Research UK, included health records from 13.9 million children under the age of 18 from January 1 2020 and December 31 2022.
During this period, around 3.9 million youngsters were diagnosed with Covid-19, while 3.4 million had the first dose of the Pfizer-BioNTech vaccine, which was the main jab to be used in five to 18-year-olds.
The team looked at the risk of rare complications such as thrombocytopenia, or low levels of platelets in the blood, clots in the blood vessels, known as arterial and venous thrombosis, as well as myocarditis and pericarditis.
Researchers found youngsters had a higher risk of these conditions up to 12 months after being diagnosed with Covid-19.
Meanwhile, the risk of myocarditis or pericarditis was higher for four weeks post-vaccine, although researchers said the risk of developing them was "substantially lower" than the risk following infection with the virus.
Dr Alexia Sampri, of the University of Cambridge, said: "Our whole-population study during the pandemic showed that although these conditions were rare, children and young people were more likely to experience heart, vascular or inflammatory problems after a Covid-19 infection than after having the vaccine - and the risks after infection lasted much longer."
Researchers estimate that over six months, Covid infections led to 2.24 extra cases of myocarditis or pericarditis per 100,000 children and young people, with this falling to 0.85 extra cases per 100,000 among those vaccinated.
Co-author Professor Pia Hardelid, of UCL and the National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre, said: "Parents and carers have faced difficult choices throughout the pandemic.
"By building a stronger evidence base on both infection and vaccination outcomes, we hope to support families and healthcare professionals to make decisions grounded in the best available data."
The team also looked at a number in inflammatory conditions, including paediatric inflammatory multi-system syndrome (PIMS), a new illness that happens weeks after someone has Covid-19 which causes swelling throughout the body, and Kawasaki disease, inflammation of the blood vessels which causes a fever, rash and swelling.
Co-author Prof Angela Wood, of the University of Cambridge and associate director at the BHF Data Science Centre, said: "After Covid-19 diagnosis, we see that the risk of inflammatory conditions was around 15 folds higher in those first weeks, and that persisted for many months, maybe just up to less than a year.
"After vaccination however, we see that risks were slightly lower than the background levels, probably likely reflecting the protective effect of vaccination here."
Co-author Prof William Whiteley, of the University of Edinburgh and associate director at the BHF Data Science Centre, added: "Parents, young people, and children need reliable information to make decisions about their health.
"Data from hospitals and GP practices are an important part of the picture because they tell us all what has happened to people looked after in the NHS."
Experts said the findings, published in The Lancet Child and Adolescent Health, "are of great importance for national policy makers and caregivers considering vaccination consent for children".
They also "support the public health strategy of Covid-19 vaccination in children and young people to mitigate the more frequent and persistent risks associated" with infection, researchers added.
Prof Wood added: "Whilst vaccine-related risks are likely to remain rare and short-lived, future risks following infection could change as new variants emerge and immunity shifts.
"That's why whole-population health data monitoring remains essential to guide vaccine and other important public health decisions."
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