BMA leaders have warned registrars and medical students that unruly conduct on marches could affect their fitness to practise in the future.
The comments follow a huge student demonstration in London last week over increasing tuition fees. Violence flared sporadically, with protesters occupying Conservative Party headquarters and smashing a number of windows.
Hundreds of medical students were among the 50,000 people on the march but, according to the BMA, were not involved in the clashes.
Dr Alex Smallwood, chairman of the GPC registrars subcommittee, said it was 'understandable' that future GPs may protest passionately but urged them to steer clear of actions that could undermine their future careers.
'You must always remember your actions can have far-reaching consequences,' he said.
'Anything other than peaceful protest shows a level of immaturity that wouldn't be becoming of a doctor.'
GMC guidance clearly states that details of student misdemeanours may be taken into account by the regulator if they are of a nature that may affect a doctors' fitness to practise.
The guidance says: 'It must be made clear to students that the GMC will consider any issue that calls their fitness to practise into question. This includes anything that happened before or during their undergraduate years and any decisions made by a fitness to practise panel or university.'
Karin Purshouse, chairwoman of the BMA's medical students committee, said there was a large turnout of students from medical schools.
The BMA fears changes to the fees universities can charge could leave future doctors with debts of up to £70,000.
'Medicine already has a low intake of people from low-income families and this will only get worse,' said Ms Purshouse. 'Medicine should be about people's ability, not their ability to pay,' she said.
Ms Purshouse added that BMA students would not condone any violence. 'There were 51,000 students and that's from a small minority,' she said.