We report on a patient carrying a de novo interstitial deletion of chromosomal region 6q23.2-24.1. Interstitial deletions of 6q are rarely reported in the literature. Indeed, only four patients with interstitial deletions overlapping partially with the deleted region in our patient are described in the literature. The aberration was detected by GTG-banding. The size of the deletion was further refined by array-CGH and subsequently fine mapped by quantitative real-time PCR. The exact size of the deletion and the sequence composition of the breakpoints were determined by breakpoint spanning PCR and subsequent sequencing. The patient presented with microcephaly, short stature, patent ductus arteriosus, sensorineural hearing loss, mental retardation, reduced speech development, and abnormal behaviour. The deletion disrupts the gene EYA4. Mutations within this gene are associated with postlingual sensorineural hearing loss. The sequencing of the breakpoint indicated non homologous end joining as the most likely mechanism leading to the rearrangement.