Background Recent case reports described three cases of holoprosencephaly (HPE) in the area with high mining-related pollution of the southern region of the Democratic Republic of the Congo (DRC). We reported two male neonates with clinically diagnosed HPE in the localities of Fizi and Kitutu, two mineral areas in the Eastern region of the same country (DRC), where artisanal surface mining is predominant with high exposure to radiation and heavy metals from mining. Cases presentations Two newborns from adult and multigravida mothers without pregnancy complication. The birth weights were 3,200 g and 2,500 g, respectively, and the malformations noticed were essentially the single median eye, the absent nose, polydactyly for one case, and proboscis for the other case. They both died a few minutes later after birth. Conclusion The etiologic factors of HPE remain unknown but seem to be multifactorial from both genetic and environmental factors. We hypothesize under reserve for these two cases that mining and radiation expositions were likely potential environmental associated factors to the occurrence of these malformations.