We present the case of a 20-year-old man referred to the clinical geneticist because of mental retardation and dysmorphic features because of concerns about hereditability when his older, healthy brother was expecting a child. Deletion of proximal 3q arm was found with standard G-banding, and array comparative genomic hybridisation (array-CGH) was used to further locate the breakpoints. A unique interstitial deletion del 3q13.11q13.33 was confirmed. The first clinical symptoms in the 20-year-old were described at the age of 4 months when the pediatrician reported muscle hypertonia of the lower limbs, which later evolved into hypotonia. Later clinical observations revealed that the patient’s psychomotor development was delayed: he exhibited craniofacial abnormalities, cryptorchidism, thoracic kyphosis, and tapering fingers. Interstitial deletions of the proximal long arm of chromosome 3 have rarely been reported:; there are only 12 previously reported cases. The breakpoints and sizes of described deletions vary greatly, which makes definite genotype-phenotype conclusions impossible at this time. Developmental delay is one of the common features described in the majority of reported cases. The BTB-zinc finger gene ZBTB20 might be a potential candidate gene: it was shown in the mouse hippocampus to be expressed during the important period of neurogenesis of pyramidal neurons. Also, four of patients reported to date had agenesis of the corpus callosum and one, holoprosencephaly. We suggest that the GAP43 gene is involved in the development of structural neurological abnormalities in patients with 3q deletion.