The aim of this paper is to explore the ethical issues and challenges that arise in the treatment of human skeletal remains in the areas of archaeology, forensic anthropology, destructive analysis, museology, and education. The existing legal framework and guidelines in the Republic of Croatia are compared with those from the United States and the United Kingdom. Examples describe specific situations and problems in practice that are largely caused by the lack of adequate legal regulations and guidelines. As human skeletal remains once belonged to living people who lived in communities and had their own beliefs and values, it should be accepted that the modes of use and work on human remains cannot simply be reduced to the ones pertaining to ordinary artefacts or materials. Therefore, it is necessary to introduce additional regulations so as to standardize the practice in all institutions in Croatia. Also, the ethics of the current treatment in professional circles and the public should be further critically inspected, as this is the only way to motivate change. Finally, a number of principles are offered that should be followed when designing new regulations in the Republic of Croatia.