The key cellular regulator p53 is a common target of viral oncoproteins. However, the mechanism by which p53 transcription regulation is modulated by Hepatitis B virus X protein (HBx) - a transcription co-factor implicated in hepatitis B virus-associated hepatocellular carcinoma (HCC) - is poorly understood. By integrating p53 ChIP-on-chip and expression profiling of a HBx-expressing cell culture system, we report that HBx alters p53 binding site selectivity at the regulatory regions of genes and this is associated with their aberrant expression. Using a HBx-deregulated gene p53AIP1 as a model, we show that HBx aberrantly increases p53AIP1 expression by conferring p53 selectivity for a more conserved binding site at its regulatory region. We further demonstrate that HBx-deregulated increased p53AIP1 expression is relevant in HCC livers and define a functional role for p53AIP1 in mediating HBx-induced apoptosis in vitro. Significantly, we provide evidence that specific p53-associated transcription cofactors and coregulators are differentially recruited in the presence of HBx, effecting a PCAF-mediated 'p53 Lys320 acetylation switch' that results in altered binding site selection of distinct p53 transcription cassettes. The findings here clarify the role of HBx in modulating p53 transcription regulation and provide a novel mechanistic insight to this deregulation.