In Sweden, freedom of conscience for health care professionals is not legally permitted. However, requests from medical students to adjust and/or skip compulsory learning activities because of their religious and moral convictions appear to get more abundant. This creates problems when learning activities are directly related to the examination objectives stated by the Higher Education Ordinance of Sweden. Allowing students to abstain from certain parts of the medical program raises difficulties as to what kind of convictions that should be accepted and to what degree. Questions arise regarding equality of learning opportunities, assessment, and reasonable resource allocation. We call for national debate regarding these issues, which different universities now are forced to handle on their own, with the aim of establishing a common approach.