Publication ethics is an important aspect of both the research and publication enterprises. It is particularly important in the field of biomedical science because published data may directly affect human health. In this article, we examine publication ethics policies in biomedical journals published in Central and Eastern Europe. We were interested in possible differences between East European countries that are members of the European Union (Eastern EU) and South-East European countries (South-East Europe) that are not members of the European Union. The most common ethical issues addressed by all journals in the region were redundant publication, peer review process, and copyright or licensing details. Image manipulation, editors’ conflicts of interest and registration of clinical trials were the least common ethical policies. Three aspects were significantly more common in journals published outside the EU: statements on the endorsement of international editorial standards, contributorship policy, and image manipulation. On the other hand, copyright or licensing information were more prevalent in journals published in the Eastern EU. The existence of significant differences among biomedical journals’ ethical policies calls for further research and active measures to harmonize policies across journals.