Allelic alterations of chromosome 18 microsatellites were determined using normal and tumor DNA pairs from 29 patients with infiltrating ductal carcinoma of the breast. Loss of heterozygosity was detected in 62% (18 of 29 patients) of the tumors at one or more of these microsatellites. Eight of the 18 patients exhibited deletions in the region at 18q21.1. This chromosomal band is known to contain a tumor suppressor gene (DCC) whose expression is frequently inactivated in several types of cancer. Ten other patients had deletions in regions not included in the DCC locus. Five of these patients revealed a common deletion at the D18S50 locus (18q23), and the other five patients had deletions in various other regions of the chromosome. No apparent correlation between loss of heterozygosity of chromosome 18 microsatellites and the clinical stage was found in this series. The results indicate that, in addition to the DCC locus, the 18q23 region is likely to contain a second tumor suppressor gene relevant to breast carcinogenesis. Four percent of all microsatellites tested in these patients showed allelic differences in the sizes of repeat units between tumor and the corresponding constitutional DNAs. The pattern of allele instability observed in breast carcinoma differed from that originally reported in a hereditary type of colorectal carcinoma. The observation suggests that this phenomenon is not a mechanism specific to neoplastic processes in breast carcinoma.