Array-based comparative genomic hybridization (CGH) provides a higher-resolution and more quantitative alternative to chromosome CGH for the assessment of abnormalities in genomic copy number. In array-based CGH analyses published to date, array elements have been composed of cloned DNA sequences (such as P1s, BACs or complementary DNAs), and thus copy number abnormalities can be mapped from data on the genomic mapping of such clones. These advanced methods are limited by difficulties in the production of cloned DNAs and distortions in the data arising from elements in the arrays that are present at multiple copies in the normal genome. To overcome some of these limitations, we have produced a low-complexity probe based on the polymerase chain reaction (PCR). In oligonucleotide array CGH, probes are prepared by multiplex PCR amplification using 10–50 primer pairs. Two 50-base oligonucleotides that map between the primer pairs serve as array elements. Because the linearity of this method apparently depends on primer complexity during PCR, we substituted adapter sequences (which make up the 5′ end of our PCR primers). We compared the performances of T7 and R24 adapters in a 24-plex PCR with one another and with previously obtained copy number data on several chromosome 20 loci in MCF7 cells obtained from fluorescence in situ hybridization. We found that use of the T7 adapters improved the amplitude of test-to-reference ratios 2.3-fold, suggesting less-dampened ratios and increased linearity in our assessment of copy number by this method. We will demonstrate the large-scale application of oligonucleotide array CGH to ovarian and breast cancer samples.