As defined initially, chromosome instability syndromes (CIS) are a group of inherited conditions transmitted in autosomal recessive pattern characterised with both mental and physical development delay generally. They are also with other medical complications in individuals with CIS commonly including different degree of dysmorphics, organs/systems dys-function and high risk of cancer predisposition. Chromosomal breakage from CIS can be seen either in spontaneous breakage around 10–15% observed in Fanconi anemia or induced by clastogenic agents such as mitomycin (MMC), diepoxybutane (DEB). The spontaneous chromosome breakage is less common but it correlates with patient clinical severity. Relative high rates of some types of CIS can occur in certain ethnic groups. Individuals with CIS are commonly in childhood and these disorders are often lethal. Diagnosis is complicated usually because the symptoms presented from individuals with CIS may be varied and complex. Advances in molecular level have identified genes responsible for such group diseases/disorders demonstrated that CIS are characterized by the genome instability, defect in DNA repair mechanisms. Latest advances in high-throughput technologies have been increasing sequencing capabilities to facilitate more accurate data for such syndrome researches. CIS are the typical rare diseases and becoming more challenges in pediatrics clinic. In the last two decades, there were no many articles to review and analysis CIS together to comparing their phenotypes and genotypes. In this article, the similarity and differences of the phenotypes and genotypes of CIS were reviewed to understanding the whole profiles of CIS to assist laboratory genetic diagnostic services in CIS and for the confirmation from the clinical referrals.