Allelic losses or imbalances affecting chromosome arm 16q appear to be early genomic abnormalities in breast carcinogenesis, because they were observed in a significant number of breast ductal carcinoma in situ lesions in our previous study (Aldaz et al., Cancer Res., 55: 3976-3981, 1995). To define the minimum region of loss of heterozygosity (LOH), we generated a high-resolution allelotype of 35 ductal carcinoma in situ cases and completed a deletion map of chromosome 16q by means of paraffin-embedded tissue microdissection and PCR microsatellite analysis of 22 markers. We observed a strikingly high frequency of LOH in 16q, with 31 of 35 tumors (89%) affected. We identified three distinctive areas with high LOH. Two areas were described previously and correspond to 16q21 and 16q24.2-qter. The third and most commonly affected area spanned the region from marker D16S515 to marker D16S504. The most affected locus was at D16S518, in which LOH was observed in 20 of 26 informative cases (77%), and we estimate that it lies in subregion q23.3-q24.1. The region of highest LOH spanned approximately 2-3 Mb, as determined by a yeast artificial chromosome contig reported to cover this region. Such a high frequency of LOH at a preinvasive stage of breast cancer suggests that a candidate tumor suppressor gene or genes at this location may play an important role in breast carcinogenesis.