We report on a young boy carrying a de novo 580 kb deletion in the 17q21.32 chromosomal band detected by array-CGH. He had multiple malformations including cardiac abnormalities, cleft palate, mental retardation, microcephaly, pronounced metopic suture and other minor facial dysmorphic features. This is the first case reported in the literature with such a small deletion in 17q21.32. This region includes 15 genes.