The comparison of freshly collected breast cancer tissue DNA with that of the matched blood specimens of 144 patients was studied, and breast tissue from 30 unrelated normal women without cancer was selected as controls. The entire BRCA1 coding sequence was amplified by PCR with primers especially designed for comprehensive mutation screening by single-strand conformation polymorphism (SSCP) analysis. Amplification and electrophoresis were repeated for the confirmation of altered migration patterns. Variant bands were subsequently cut from gels, resuspended in distilled water, subjected again to PCR, and then sequenced. The amplified fragments of exon 2 and exon 3, which were not suitable for SSCP (>300bp) were sequenced directly. A total of 20 nucleotide alterations were observed in the breast cancer tissue DNA, and all were single-base substitutions. Sixteen missense mutations (which change the coding from one amino acid to another) have been identified throughout the gene. Ten cases of single nucleotide changes in BRCA1 detected in the study without records in the BIC database consisted of two missense mutations in exon 5 (273C>G, 287A>T), one polymorphism in exon 11 (2630T>G), three missense mutations in exon 11 (2532T>G, 3191C>G, 3876C>A), one missense mutation in exon 12 (4285G>A), two missense mutations in exon 17 (5115T>C, 5116A>G), and one missense mutation in exon 18 (5206T>A). The same analysis was carried out on matched blood specimens for each of the 20 nucleotide alterations revealed to be present in the germline. No nucleotide alterations were detected in the controls. These results suggest that somatic mutations of BRCA1 are infrequent in sporadic breast cancer, and nucleotide alterations were more easily observed in the breast cancer tissue DNA. It is likely that there are other important susceptibility genes that remain to be identified in patients with sporadic breast cancer.