Through several large-scale screening studies for autism spectrum disorders (ASD), a common 593-kb interstitial deletion of 16p11.2 has been identified as one of the most common genomic disorders associated with ASD. In this study, a familial occurrence of the 16p11.2 deletion was identified in association with hemivertebrae. The proband was a 3-year-old boy who showed developmental delay, displayed hyperactive but not autistic behavior, and had hemivertebrae, rib anomalies, and inguinal hernia. Familial investigation revealed that his mother shared the same deletion. Under the hypothesis of the existence of an unmasked mutation in the deletion region, we analyzed the sequence of the T-box 6 gene (TBX6) included in the deletion region, but did not detect any mutation. This suggests that haploinsufficiency of TBX6 can lead to vertebral malformation in low penetrance.