BACKGROUND: The purpose of this study was to examine a human fetus with combined holoprosencephaly and cyclopia by means of histology and 3-D reconstruction to determine the internal structure and extent of the malformation. METHODS: The head from a human fetus at 20 weeks gestation and a diagnosis of holoprosencephaly and cyclopia was investigated histologically and three-dimensionally reconstructed with CAD techniques. The cranial bones, blood vessels, nerves, eye and brain anlagen were reconstructed. RESULTS: The 3-D reconstruction revealed both severe malformation and absence of the facial midline bones above the maxilla, and a malformation of the maxilla and sphenoid bone. The mandible, posterior cranial bones, cranial nerves and blood vessels were normal. A synophthalmic eye with two lenses was found. The prosencephalon was a single small protrusion above the diencephalon. No nasal cavity was present. Above the single eye a proboscis was found. CONCLUSION: The absence of the facial midline bones above the maxilla and the presence of a proboscis as a nose-like structure above the cyclopic eye both mean that there was a developmental defect in the fronto-nasal facial process of this fetus.