Miller-Dieker syndrome represents a microdeletion syndrome spanning the LIS1 locus at 17p13.3, the deletion of which leads to lissencephaly. A fluorescence in situ hybridization study using an LIS1 probe is considered the standard laboratory diagnostic method for Miller-Dieker syndrome. This report documents a Miller-Dieker syndrome patient who tested normal when a commercially available LIS1 fluorescence in situ hybridization study probe was used but was later demonstrated to have a partial deletion of the LIS1 locus. The present case exemplifies a major shortcoming of commercially available fluorescence in situ hybridization studies for the diagnosis of microdeletion syndromes such as Miller-Dieker syndrome: that is, relatively small deletion can potentially remain undetected.