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 5.5-5.8Mb. This single family report highlights the mild phenotypes that can be associated with duplications of chromosomal regions, even those that are larger than 5Mb and harbor known disease-related genes, and highlights the impact of identifying balanced carrier status in a parent for accurate genetic counseling.