Due to the lack of robust diagnostic methods and limited resolution of conventional microscopy, submicroscopic genomic duplication copy number variants (CNVs) have been long underascertained. The development of array CGH has enabled detection of microduplications with nearly the same sensitivity as microdeletions and thus allowing them to be routinely identified throughout the human genome. However, in contrast to microdeletions, clinical interpretation of microduplications more often presents a diagnostic dilemma, as the functional impact of these genomic alterations is not well understood. Microduplications are especially difficult to interpret when they encompass several genes or a portion of a gene. Determining their significance involves investigative teamwork between both the diagnostic laboratory and the clinician. We present the steps for interpreting the clinical significance of microduplications and representative examples of these challenging cases. © 2010 Wiley-Liss, Inc.