PURPOSE: Array-CGH is the technique for detecting multiple chromosomal abnormalities in the genomic DNA with using a single procedure. Compared with conventional CGH, there are many advantages for array-CGH such as high resolution, simplified image analysis and high throughput, and its oligo-strategy allows a genome based design. We analyzed the gene aberrations in breast cancer patient to discover the other genomic aberrations that are associated with c-erbB-2 amplification. METHODS: 10 cases of breast cancer patients, considering its c-erbB-2 status of the paraffin embedded tissues, were analyzed with performing array-CGH. RESULTS: The repeated aberrations in whole cases were found in 78 loci, of which repeatedly gained in 1p36.33, 19p13.13, and lost in 14q32.33, 4q32.3, 10p15.3, 14q21.1. The unsupervised dendrogram couldn't show significant classifier for its limited case number. Each tissue from one bilateral breast cancer patient showed a different aberration pattern. There were no BRCA1, 2 aberrations in this study. The concordance was 100% between the IHC and the a-CGH. By the supervised clustering on the c-erbB-2 factor, 18 aberrations (gained in 17q12-21.1, 17q12, 17q21.1, 17q11.2 and lost in 22q11.1, 15q11.2) were found in c-erbB-2 (+) group with the permutation t-test. The repeated aberrations of c-erbB-2 (+) group were found in 170 loci, of which repeatedly gained in 17q12, 17q21.1 and lost in 14q32.33, 22q11.1. CONCLUSION: Although the number of cases was small, performing a-CGH with paraffin embedded breast cancer tissue was a useful technique for rapidly identifying DNA aberrations with high throughput, and this technique showed significant aberrations for some clinical variables.