The objective of this study was to demonstrate that the branchiooculo-facial (BOF) syndrome is a cervicocephalic neural crest maldevelopment. Using an embryologic study, we linked the clinical features and the level of the neural crest deficiency. We report here two cases of BOF syndrome with a particular branchial cleft presenting as bilateral supernumerary thymus glands on the surface of the skin; one of the cases was associated with tetralogy of Fallot. One patient underwent lip reconstruction at 4 months, combined with excision of bilateral auricular pits and superior labial fistula. The other patient had a surgical correction of the tetralogy of Fallot, and at 2 months, the two stages of the lip reconstruction were performed, combined with bilateral auricular pit excision. Both patients have shown normal developmental patterns to date. The BOF syndrome must be considered as a neurocristopathy at different levels, with a tiny mesencephalo-prosencephalic lesion and a severe rhombencephalic lesion that includes seven consecutive hindbrain segments, from rhombomere 2 to rhombomere 8.