Distal chromosome 3p deletions (3p- syndrome) are associated with various developmental defects. The majority of cases have a terminal deletion of the short arm of chromosome 3 with loss of either the maternal or the paternal copy. A girl with an interstitial molecularly characterized 1.6 Mb deletion in cytoband 3p25.3-26.1 of the paternal chromosome 3 is presented. To our knowledge, she possesses the smallest deletion that has ever been reported for a patient with a clinical phenotype in accordance with the 3p- syndrome. The boundaries of the deletion lies within nearly all previously reported terminal deletions causing this syndrome. Selected genes that are present in the hemizygous state and which might be important for the phenotype of this patient as regards the congenital heart defect, autistic behavior and mental retardation (CAV3, OXTR, and SRGAP3/MEGAP, respectively) are discussed in context of the clinical features. © 2010 Wiley-Liss, Inc.