Chromosomal abnormalities caused by genomic instability are a consistent feature of cancer cells. However, the mechanisms that lead to genomic instability and its role in cancer progression, and ultimately clinical outcome, are not well understood. Advances in whole genome sequencing and other high-throughput molecular techniques have vastly improved our ability to characterize cancers. Researchers have begun to measure genomic/chromosomal instability (GI/CIN) by using multiple data types, including copy number, gene expression, and somatic mutations. These measures of instability have been associated with various clinical outcomes, but results have been inconsistent. Several methods for creating summary measures of CIN have been published, but there is no consensus about the best method. Additionally, it is unclear whether any one method is appropriate for all cancer types. Current methods also do not take advantage of information about specific cytogenetic abnormalities that are recurrent in specific cancer types. Given the potential clinical value of CIN as a predictor of cancer progression or treatment response, there is a critical need to better understand how best to summarize measures of CIN.