Loss of heterozygosity (LOH) was analyzed in 113 cases of sporadic breast cancer using 35 microsatellite markers on 20 chromosomes. LOH was frequently seen in 17p (44%), 16q (31%), 17q (29%) and 13q (23%). Individual patients were scored according to the incidence of LOH at the above four chromosomal markers; with no LOH as 1, with one or two LOH as 2, and with three of four LOH as 3. A high LOH score was well associated with high histological grade (p = 0.019) and a significantly poor prognosis (p = 0.0035). These data suggest that accumulation of LOH occurs at a later stage of breast cancer progression, and that the LOH score may be a useful prognostic marker of breast cancer.