Pathological findings in two patients with Moebius syndrome and lethal fetal akinesia sequence are described. In both patients a congenital brain stem malformation with neuronal loss in the cranial nerve nuclei and tegmental microcalcifications was observed. In one patient, the association with splenogonadal fusion was observed, whilst in the second patient, the association with tetraperomelia was present. As the association of peromelia and splenogonadal fusion is a well-known association, the different combination of splenogonadal fusion, peromelia and Moebius syndrome due to congenital brain stem anomalies with necrosis might be the result of a disruptive phenomenon during a prolonged vulnerable critical period in the 5th and 6th week of embryonic life. The finding of olivary dysplasia in one case, reminiscent of olivary dysplasia in Zellweger syndrome and in Miller Dieker syndrome, might suggest a primary malformation underlying Moebius syndrome due to brain stem defects.