Subtelomeres are an incredibly dynamic part of the human genome located at the ends of chromosomes just proximal to telomere repeats. Although subtelomeric variation contributes to normal polymorphism in the human genome and is a by-product of rapid evolution in these regions, rearrangements in subtelomeres can also cause intellectual disabilities and birth defects, making robust methods of detecting copy number variation in chromosome ends a must for cytogenetics labs. In recent years, methods for detecting structural variation in subtelomeres have moved from fluorescence in situ hybridization (FISH) to array technology; however, FISH is still necessary to determine the chromosomal structure of subtelomeric gains and losses identified by arrays.