This paper analyzes conscientious objection by physicians, with the concrete situation of legal abortion in Brazil. The study reviews the two main ethical frameworks about conscientious objection in public health, the incompatibility thesis and the integrity thesis, in order to analyze the reality of legal abortion services in the Brazilian public healthcare system. From these two perspectives, a third one is presented — the justification thesis, to manage the right to conscientious objection among physicians in public healthcare services. This analysis may contribute to the organization of services for legal abortion and to the education of physicians working in emergency obstetric care in the future.