We report on the clinical and array-based characterization of an interstitial 1p31.3 deletion in a 15-year-old male patient with obesity, behavioral problems including multiple psychiatric diagnoses, mild intellectual impairment, facial dysmorphism, and a strong family history of psychiatric illness. The deletion breakpoints were determined by molecular karyotyping, revealing a 3.2 Mb excision. Patients previously reported with hemizygous deletions including this cytogenetic band had intellectual impairment and some facial features that overlap with our patient's phenotype. However, their deletions were larger, encompassing several cytogenetic bands, making this case the smallest deletion to date that we are aware of sharing these phenotypic characteristics. There are 17 genes that map to the interval. Two genes within the interval, LEPR and PDE4B, are interesting candidates for these phenotypes because of their potential role in obesity and psychiatric illness, respectively. Identification of the smaller deletion underscores the importance of combining clinical investigation and array comparative genomic hybridization analysis for appropriate diagnosis, genetic counseling and potentially for prenatal diagnosis. © 2011 Wiley-Liss, Inc.