More than half of the reported missense changes in the breast cancer susceptibility protein BRCA1 occur in exon 11, but none has been clearly identified as disease associated and only 28 are designated 'probable' neutral polymorphisms. Previously, in a comparison of sequences from 57 eutherian mammal species, we found seven 'highly conserved regions' between amino acids 282 and 1103, and identified 38 missense changes as likely to disrupt gene function. These conserved regions were also present in birds and amphibians and included only six of the mutations predicted to affect function. In this new analysis, we hypothesized that using 37 ancestral sequences derived from the 57 GenBank sequences and including eight marsupial sequences would allow us to identify regions unique to mammals and refine our predictions of disease-associated missense changes. We identified 13 conserved regions, three of which appear to be unique to mammals, and 21 likely disease-associated missense changes, 11 of which occur in conserved regions. Seven regions identified in this analysis, including the three found only in mammalian sequences, and nine missense changes predicted to affect function are in the putative STAT1-interaction domain, suggesting that the role of STAT1 in immune response is important to mammary function. The reduction in the number of missense changes predicted to be disease associated and the identification of conserved regions specific to mammals can facilitate the further study of the role of missense changes in BRCA1-associated breast cancers.