Congenital malformations of the central nervous system [CNS] are common birth defects that have devastating effects on the individual, family and society. The study was conducted with the aim of studying the genetics of CNS malformations as well as to determine the relation between CNS malformations and inbreeding. The study included 104 patients. Microcephaly was present in 45 patients [43.2%] of which 37 patients [35.6%] had single gene defects, 7 patients [6.7%] had a chromosomal abnormality while one patient [0.9%] was born to a diabetic mother. Neural tube defects [NTD] were present in 32 patients [30.8%], whereas macrocephaly was present in 11 patients [10.6%] all were the result of storage disorders. Congenital hydrocephaly was present in 9 patients [8.7%], while holoprosencephaly [HPE] was present in 7 patients [6.7%]. The frequency of consanguineous mating among parents of children with CNS malformations was 48.1% a value significantly higher than that of the general population. Parental consanguinity was significantly higher in patients with microcephaly, macrocephaly and congenital hydrocephaly. The average inbreeding coefficient in patients with CNS malformations was twice that of the Egyptian population. It was especially elevated in patients with microcephaly, macrocephaly and hydrocephaly reflecting increased homozygosity