We characterized a t(1;7)(p22;q21) reciprocal translocation in a patient with childhood-onset schizophrenia (COS) and autism using genome mapping and sequencing methods. Based on genomic maps of human chromosome 7 and fluorescence in situ hybridization (FISH) studies, we delimited the region of 7q21 harboring the translocation breakpoint to a approximately 16-kb interval. A cosmid containing the translocation-associated 1:7 junction on der(1) was isolated and sequenced, revealing the positions on chromosomes 1 and 7, respectively, where the translocation occurred. PCR-based studies enabled the isolation and sequencing of the reciprocal 7:1 junction on der(7). No currently recognized gene on either chromosome appears to be disrupted by the translocation. We further found no evidence for copy-number differences in the genomic regions flanking the translocation junctions in the patient. Our efforts provide sequence-based information about a schizophrenia/autism-associated translocation, and may facilitate future studies investigating the genetic bases of these disorders.