The spectrum of genetic alterations in primary male breast cancer is not well established. We analyzed chromosomal imbalances in 39 tumor samples from primary male breast cancer by comparative genomic hybridization (CGH) and correlated CGH findings with clinicopathological factors. Chromosomal gains were most frequent at 1q (46%), 8q (46%), 16p (36%), 17q (36%), Xq (28%), 20q (26%) and Xp (18%). Losses were most commonly observed at 8p (36%), 16q (28%), 13q (28%), 6q (18%), 11q (18%) and 22q (18%). Gains at 16p, 20q and Xq and losses at 13q correlated significantly with higher degree of cytogenetic complexity. Significant associations with clinicopathological factors were observed for 18q and 216q with larger tumor size and 216q with lower proliferative activity and lower grade of malignancy. A comparison with reported CGH data from female breast cancer showed a similar pattern of chromosomal imbalances, including 11q, 28p, 18q, 213q, 116p, 216q, 117q and 120q. Our results indicate that male breast cancer shares a common pattern of imbalances with female breast cancer, suggesting that similar genetic events may underlie the development and progression of male and female breast cancer. ' 2005 Wiley-Liss, Inc.Key words: male breast cancer; comparative genomic hybridization; genomic aberrations Male breast cancer is an uncommon disease, accounting for 1% of all breast cancer cases. 1 The phenotypic characteristics are not well studied, and are mainly inferred from female breast cancer. Although both diseases share similarities, there are notable differences in risk factors, prognosis and survival. 2 Most male breast cancers are estrogen receptor (ER) and progesterone receptor (PR) positive 1 and expression levels of the HER-2/neu receptor are typically low. 3 The vast majority are ductal tumors and lobular tumors are rare. 4 The comparably unfavorable outcome in male breast cancer has been attributed to more advanced local tumor stages and high incidence of lymph node invasion. It has been postulated that close proximity to skin and nipple facilitates early invasion of lymph vessels, leading to earlier regional and distant metastasis. 5 Germline BRCA2 mutations account for a significant part of male breast cancer, but the majority of patients lack a known inherited predisposition. 6 As in women, axillary lymph node status, tumor size, histological grade and hormone receptor status have been proposed to be the prognostic factors in men with breast cancer. 1 Data regarding more recent molecular markers and their prognostic significance in male breast cancer are limited. The identification of genetic changes and new molecular markers in male breast cancer may provide insights into the biologic differences between male and female breast cancer patients and could aid in clinical management. 7 So far, data on the presence of specific genetic alterations in male breast cancer are limited. Most of these studies are focused on the analysis of germline mutations.No comprehensive molecular cytogenetic study on male breast ca...