In Personal Beliefs and Medical Practice, GPs are advised to make it clear to patients if they object to certain treatments, like abortion.
GPs must make sure the patient is aware of their right to see another doctor. Failure to do so could affect a GPs registration, the document says.
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 not many practices would be affected.
The guidance also responds to controversial issues like 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.
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