Genomic alterations affecting chromosome arm 1q are considered to be an early event in breast carcinogenesis and are correlated with good prognosis for the patients. In the search for new breast cancer susceptibility genes, we focused on three genes from the Regulator of G protein Signaling family clustered on 1q25.3 within the HPC1 region. RGS16, RGSL2, and RGSL1 encode proteins interacting with G proteins and accelerating termination of the G protein signaling. To evaluate the implication of these genes in somatic breast cancer, we analyzed a 154-kb segment at 1q25.3 using allelic imbalance (AI) mapping. A panel of 222 patients diagnosed with primary breast cancer was analyzed using newly identified, intragenic short tandem repeats (STRs). A high rate of AI (>50%) was found across the region and led to the identification of internal chromosomal breakpoints. A detailed mapping of the breakpoints revealed intragenic microdeletions affecting the coding regions of RGSL2, RGSL1, and the regulatory region of RGS16. The promoter region of RGS16 was found to be methylated in 10% of the tumors. A decrease in the RGS16 expression was found in tumors with chromosomal breakpoints, AI, and aberrant methylation. We found a significant association between AI of RGSL2 and localized disease, which correlated with good prognosis for patients with breast cancer. In conclusion, we found the 1q25.3 region to be highly unstable in breast tumors comprising a cluster of chromosomal breakpoints, intragenic microdeletions, frequent allelic imbalance correlating with long metastasis-free survival, and RGS16 promoter methylation affecting the protein expression. © 2008 Wiley-Liss, Inc.