One of the central dogmas of the Catholic Church is the belief in the Eucharistic presence of Jesus Christ, which requires no scientific confirmation because it concerns a supernatural reality. Since the early Middle Ages, however, instances have been recorded improperly referred to as Eucharistic miracles, which believers consider eyewitness testimony to a real transubstantiation. Changes in the structure, number, or an unexpected bloody red colour of the Host were often regarded as supernatural phenomena, but the Church officials themselves, aware of the possibility of a biological basis for these changes, showed far-reaching restraint. The author's team on the basis of analyses of 25 actual cases undertook to prepare research procedures that make it possible to separate phenomena that are difficult to interpret scientifically, from those associated with contamination. None of these cases revealed the actual proof of existence of human blood, human material other than single epidermal cells, and erythrocytes (probably very low-level contamination). In one case, insignificant amount of human male genetic material was observed, probably as a result of DNA transferred from a person to a host via contact with the host itself. In several specimens, a variety of microbial and fungal material was identified (Brevundimonas intermedia, Serratia marcescens, Epicoccum spp,. Fusarium spp.), including species producing reddish-pink or orange-reddish pigments (Epicoccum spp., Fusarium spp.). Based on the experience gained in this study, a complete procedure suitable for reliable examination of similar cases in the future is suggested. KEY POINTS: • The unusual appearance of the tested hosts can be explained by biological contamination. • Blood-like marks result from the presence of pigment-producing species. • A complete multidisciplinary procedure for investigating 'miracle cases' is proposed.