More than 100 cases of deletions that span 11p13-11p14 resulting in WAGR syndrome have been reported in the literature. In contrast, reports of duplications spanning this region are extremely rare. We here report on a deletion of 11p13-11p14 identified in a neonate with severe congenital anomalies including genitourinary abnormalities and aniridia, and the reciprocal duplication identified in his healthy older sibling. Both were derived from a paternal balanced insertion of the 11p region into 18q. The deletion and duplication were characterized by G-banding, FISH and array CGH, and are estimated to include approximately 5.5–5.8 Mb. This single family report highlights the mild phenotypes that can be associated with duplications of chromosomal regions, even those that are larger than 5 Mb and harbor known disease-related genes, and highlights the impact of identifying balanced carrier status in a parent for accurate genetic counseling. © 2011 Wiley Periodicals, Inc.