| Type of encephalocele | Differential diagnosis |
| Occipital encephalocele | Midline dermoid cysts |
| Hemangiomas | |
| Vascular malformations of the scalp | |
| Cystic hygroma | |
| Cranial vault | Congenital parietal foramina |
| Scalp defects (aplasia cutis congenita) | |
| Dermoid cysts | |
| Hemangiomas | |
| Frontoethmoidal and basal | Dermoid cysts |
| Hemangiomas | |
| Sinus pericranii | |
| Basal | Inflammatory nasal polyps |
| Atretic cephaloceles | |
| Mucocele of the paranasal sinuses | |
| Neoplasms of the nasal cavity and pharynx | |
| Spheno-orbital or frontosphenoidal | Orbital teratoma |
| Unilateral agenesis of the sphenoid and orbital plate (eg, in neurofibromatosis I) | |
| Congenital cystic eye |
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