In 'Personal Beliefs and Medical Practice', published this week, the GMC warns GPs to make it clear to patients if they object to treatments, such as abortion, to ensure that a professional's beliefs do not influence a patient's treatment.
Patients wanting a procedure to which a GP objects on personal grounds must be made aware of their right to see another doctor. Failure to do so could affect a GP's registration, according to the document.
Both the GMC and the Medical Defence Union said they were receiving a growing number of queries relating to clashes between best practice and the personal beliefs of doctors and patients.
But GPC deputy chairman Dr Richard Vautrey said such cases were unusual and affected few practices.
'By drawing attention to one aspect of their practice, it can mean a GP is seen unfavourably regardless of their other treatments,' he said.
'It is important to highlight the individual cases but we don't want to make this into an issue for everybody.'
The guidance also responds to controversial issues such as circumcision and the wearing of face veils by Muslim doctors.
On both issues the GMC states it has no clear position on the matter, but provides guidance on how to assess what is best for the patient.
Comment below and tell us what you think