We hypothesize that copy number variants (CNVs) contribute to the location of schizophrenia linkage regions. Therefore, we test whether CNVs published by the International Schizophrenia Consortium are enriched in schizophrenia linkage regions recorded in the Online Mendelian Inheritance in Man database. For each region, the number of overlapping CNV events and the number of CNV base pairs are compared with 10 000 random regions of matched size. This shows an enrichment of CNV events within the linkage regions SCZD4 (22q11), SCZD10 (15q13-q14) and SCZD12 (1p36) for both cases and controls. The magnitude of this genomic enrichment of CNV event is more pronounced among cases for SCZD10 and SCZD12, whereas the number of CNV base pairs is greater among cases for SCZD4 and SCZD10. These results are consistent with a higher mutability that has produced an increased CNV burden in these regions in both cases and controls, with CNVs being more likely to be deleterious among cases.