We describe a 46-month-old child presenting with developmental delay, mild facial dysmorphism, micropenis, strabismus and striking multiple cysts of the corpus callosum who was found to have a de novo interstitial 3.1 Mb 15q24.1q24.2 microdeletion using a 244 K microarray-based comparative genomic hybridization (array-CGH). The cystic lesions were located in the anterior half of the corpus callosum and did not take up gadolinium contrast. There was no other brain abnormality, and the gyral pattern and myelination were normal. There was no history of infectious disease or vascular injury and a metabolic disease was ruled out. Such cystic lesions of the corpus callosum are exceptional in the pediatric literature. Although these brain abnormalities have not been described in other reports with 15q24 microdeletion, we believe that they might be related to the cytogenetic abnormality since the work-up for other causes was negative. We suggest that a chromosomal rearrangement should be ruled out when such corpus callosum lesions are identified. © 2009 Wiley-Liss, Inc.