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In historically Protestant countries, human skeletal reference collections curated by research institutions have been amassed from bodies dissected by anatomists, typically unclaimed cadavers from morgues and hospitals, or from remains donated to science. In contrast to these anatomy-based and donation-based collections, skeletal reference collections in historically Roman Catholic countries on mainland Europe and in Latin America are for the most part derived from unclaimed remains exhumed from modern cemeteries and ossuaries at the end of the mandated interment period. While much has been written in English about the history, context and ethical framework of anatomy-derived collections, cemetery-based collections have received very little critical attention. The current paper addresses this gap, with particular reference to cemetery-derived collections in Portugal. The cultural and historical context of southern Europe is discussed, particularly Roman Catholic mortuary traditions and the influence of the Napoleonic Code, and these provide the background for an overview of the ethical issues raised by cemetery-derived collections. Here, general principles that should guide the work of human osteologists working in archaeological contexts are relevant, as regards consent, dignity and respect and benefits to science and education, because unlike their anatomy-derived counterparts, cemetery-based collections include individuals who were once buried.