In Bulgaria, about 2,100 children are born with congenital malformations annually. Most malformations are present at delivery and are due to genetic and non genetic factors [1]. They occur at a relatively constant population frequency of 2-4% independent of race, culture and social-economic environment, and are observed in 15-20% of stillborn infants. About 60% of infants with malformations are diagnosed during the first month of life and about 80% by the end of the third month. With the introduction of ultrasonography in the routine clinical examination of pregnancy, severe congenital anomalies can be diagnosed antenatally [2], but many congenital defects cannot be diagnosed during pregnancy. About 20-25% of congenital malformations are considered to be multifactorial, and 10-13% are due to environmental factors such as infection, drugs or maternal disease [3,4]. The rest have no known cause. Chromosome abnormalities have long been recognized as an important cause of multiple malformation syndromes, 7-10% of infants with abnormal phenotype having numerical or structural chromosomal aberrations [5]. Their identification is important for accurate diagnosis and genetic counseling.The most frequent structural chromosomal abnormalities include unbalanced translocation, duplication, deletion, isochromosomes, ring chromosomes and micro-structural aberrations [5]. Some are so minor that they cannot be diagnosed by classical karyotyping. These include micro deletions or microduplications, some of them being associated with recognizable syndromes. The affected regions on the chromosome include genes which may contribute separately or simultaneously to the characteristics of the phenotype [6]. We have studied four patients with normal karyotypes who suffered from congenital malformations with or without mental retardation, by means of array-based comparative genomic hybridization (CGH) to detect microstructural genomic abnormalities and/or polymorphic regions.