The p53-upregulated modulator of apoptosis (Puma) and Noxa, are direct targets in p53-mediated apoptosis localized to the mitochondria. Tumor suppressor p53 induces apoptosis by transcriptional induction of Puma and Noxa, which encode proapoptotic BH3-only member Bcl-1 family proteins. However, at a molecular level, the mechanism of action of Puma and Noxa proteins remain poorly defined. In addition, there have been no reports on whether or not p53 directly interacts with Puma and Noxa, in vitro. Here, we provide evidence indicating that the DNA binding domain (DBD) of p53 directly interacted with the BH3 domains of human PUMA and NOXA. Our studies revealed that PUMA has a weak affinity for p53, but NOXA has significant affinity for p53. In this study, we developed a molecular docking model using homology modeling based on the structures of truncated p53, PUMA and NOXA. In addition, we investigated whether or not six mutants of p53 (K101A, T102A, L111A, D186A, G199A and S227A) were able to bind to PUMA and NOXA. Four structure-based mutations (T102A, L111A, D186A and G199A) disrupted the p53-PUMA/NOXA interaction. Our study suggested that these four mutations lowered the stability of the p53 DBD domain and induced aggregation of structurally destabilized p53, and thus disrupted the p53-PUMA/NOXA interaction.