All agree that copy number variation (CNV) contributes substantially to human genetic diversity. But to what extent? The resulting applications of newly developed whole-genome scanning technologies have catalyzed the appreciation of CNV in the genetic community. The range of these promising new technologies will, for the first time, allow scanning of the entire human genome for CNV in a single experiment. As these genome-wide scanning techniques become more widely used in diagnostic laboratories, the major challenge is how to accurately interpret which submicroscopic genomic imbalances are pathogenic in nature and which are benign.