The most frequent alteration detected in breast cancer cells is an inactivation of the tumor protein p53. Numerous studies revealed that p53 mutations are an independent prognostic indicator of a shorter period of overall and disease-free survival. Meta-analysis of these investigations clearly showed that prognostic significance cannot be achieved by indirect assessment of the p53 status by immunohistochemistry. Therefore, the tumor RNA-based functional p53 assay in yeast (functional assay of separated alleles in yeast, FASAY) appears to be an attractive option to generate clinically relevant information without the need of microdissection. We describe FASAY analyses of 50 biopsies taken before pre-operative anthracycline/taxane chemotherapy to evaluate the predictive value of p53 mutations for this common combination of substances. Wild-type p53, present in 22 samples, resulted in numerous white colonies with a low background of red colonies that was consistently below 8%. Biopsy samples containing mutated alleles gave rise to many red colonies accompanied with variable numbers of white colonies. With one single exception, all biopsies containing mutated p53 resulted in more than 8% red colonies. In 25 samples (53%), 23 single and 2 double mutations of the p53 gene were confirmed by sequencing of DNA from the yeast colonies. Six of the observed sequence insertions or deletions and 2 of the point mutations have not been reported previously. In accordance with an abolished or altered function as a transcriptional activator, most mutations affected the p53 DNA-binding domain, and one the tetramerization domain. Our results confirmed that the FASAY is sufficiently reliable to detect p53 mutations in breast tumor biopsies. In this pilot study with a limited number of patients to evaluate the predictive value of p53 mutations for an anthracycline/taxane combination therapy in the neoadjuvant setting, stable disease was observed more often in patients with wild-type p53 but statistical significance was not quite reached for this clear trend.