Capillary array electrophoresis and laser-assisted microdissection, which provide increased speed and accuracy in loss of heterozygosity studies, are often used independently in studying breast cancer; the successful coupling of these emerging technologies, however, must overcome technical problems, especially those related to the poor quality and quality of DNA typically retrieved from archival tumor samples. Here we present a panel of 52 microsatellite markers from 26 of the most commonly deleted regions in breast cancer. All markers have been optimized to robustly amplify DNA extracted from paraffin-embedded samples, represent informative (highly polymorphic) loci, and effectively detect chromosomal loss. In the 10 tumor samples (stage 0 to stage III) tested here, chromosomal loss was detected loss for every locus, and the degree of loss at the 26 commonly deleted regions ranged from 23% to 77%. This panel can be used to quickly detect genomic patterns of loss in large numbers of breast tumor samples and may provide both clinical information and molecular information regarding the underlying tumor suppressor genes.