As a result of the increasing use of genome wide telomere screening, it has become evident that a significant proportion of people with idiopathic mental retardation have subtle abnormalities involving the telomeres of human chromosomes. However, during the course of these studies, there have also been telomeric imbalances identified in normal people that are not associated with any apparent phenotype. We have begun to scrutinise cases from both of these groups by determining the extent of the duplication or deletion associated with the imbalance. Five cases were examined where the telomere rearrangement resulted in trisomy for the 16p telomere. The size of the trisomic segment ranged from ∼4-7 Mb and the phenotype included mental and growth retardation, brain malformations, heart defects, cleft palate, pancreatic insufficiency, genitourinary abnormalities, and dysmorphic features. Three cases with telomeric deletions without apparent phenotypic effects were also examined, one from 10q and two from 17p. All three deletions were inherited from a phenotypically normal parent carrying the same deletion, thus without apparent phenotypic effect. The largest deletion among these cases was ∼600 kb on 17p. Similar studies are necessary for all telomeric regions to differentiate between those telomeric rearrangements that are pathogenic and those that are benign variants. Towards this goal, we are developing "molecular rulers" that incorporate multiple clones at each telomere that span the most distal 5 Mb region. While telomere screening has enabled the identification of telomere rearrangements, the use of molecular rulers will allow better phenotype prediction and prognosis related to these findings. U nbalanced submicroscopic telomere rearrangements are a significant cause of idiopathic mental retardation with or without congenital malformations, accounting for approximately 5% of these cases. [1][2][3][4][5][6][7] With the development of a second generation set of telomere specific clones, 8 telomere screening is now readily available in many laboratories and is being used extensively in the evaluation of children with mental retardation and congenital anomalies. The results of these investigations are not only providing explanations for previously unexplained cases of mental retardation, but are also further defining the frequency of telomeric rearrangements in various clinical populations and clarifying the phenotype associated with these rearrangements. Furthermore, during the course of these studies, telomeric imbalances have also been identified in normal subjects without any apparent phenotype.3 5 6 9 These observations suggest that not all telomere imbalances result in a phenotype and that the lack of phenotypic effect may be related to the size of the rearrangement or the involvement of regions of the genome that are tolerant to dosage imbalances.Despite these advances, there is a paucity of information regarding the genotype/phenotype correlations of many of the telomere imbalances discovered, complicating t...