Medical practice implies the controversial encounter of diverse circumstances in which eventual conflicts between physicians and patients values as well as between physicians values and legal or institutional rules arise. When dealing with these situations, physicians have the right to refuse acting against their moral conscience. This conscientious objection, accepted as a personal right and recognized by several legislations and medical ethics codes, is valid only if it has been reasonably justified and declared in advance. Conversely, it would be invalid if it is based upon convenience or understood as a collective refusal, which may be a form of civil disobedience. Conscientious objection in medicine is considered a limited right even though patients ought to be respected in their demands for legally accepted treatments or interventions. On the other hand, personal conscientious objection is different from the prerogative of institutions to establish their own regulations according to their institutional ideology or ethics codes. However, public hospitals have to offer all treatments or interventions legally allowed, since the state has the obligation to guarantee all citizens an appropriate access to them.