We describe another patient with the combination of apple peel intestinal atresia, microcephaly, microphthalmia, and anterior eye chamber anomalies. Development so far seems to be normal, although there is major visual impairment due to the corneal clouding. Mutation analysis of the PAX6, FOX1, PITX2, and MYNC genes was normal as was MLPA for these genes. Autosomal recessive inheritance is possible as recurrence in sibs was described, although germ line mosaicism or a microdeletion due to a very small parental translocation cannot be ruled out.