Microdeletion syndrome is a syndrome caused by a chromosomal [[deletion]] smaller than 5 million base pairs (5 Mb) spanning several genes that is too small to be detected by conventional cytogenetic methods or high resolution karyotyping (2–5 Mb).

Detection is done by fluorescence in situ hybridization (FISH). Larger chromosomal deletion syndromes are detectable using karyotyping techniques.