The majority of cases of the two distinct disorders Prader-Willi syndrome (PWS) and Angelman syndrome (AS) result from cytogenetic deletions of chromosome 15q11-q13. These deletions are exclusively of maternal origin in AS but of paternal origin in PWS indicating that the 15q11-q13 region is subject to genomic imprinting. Transmission of a submicroscopic deletion in one three generation family resulted in AS only upon maternal transmission of the deletion with no clinical phenotype associated with paternal transmission (1,2). The breakpoint of this submicroscopic deletion has been cloned and sequenced. This is the first deletion junction from the AS/PWS region which has been so characterized. The nucleotide sequence of the deletion junction revealed a 19 bp insertion of unknown origin with no evidence of repetitive elements. A probe from the proximal deletion breakpoint, PB11, lies within the currently defined minimum region of deletion overlap in PWS, which contains the SNRPN and D15S63 loci. Our results suggest that the imprinted gene(s) responsible for the PWS phenotype are proximal of pB11 in this deletion overlap region.