The widely used antiepileptic drug valproic acid (VPA), which is also used in migraine prophylaxis and the treatment of bipolar disorders, is also under trial as an anticancer agent. Despite its wide range of therapeutic applications, VPA also has two severe side effects: acute liver toxicity and teratogenicity. The mechanism of action for all these properties is unknown to date, but recently, it was shown that VPA is able to inhibit the enzyme class of histone deacetylases (HDACs), proteins with a fundamental impact on gene expression and therefore possible molecular targets of VPA-induced signaling cascades. The purpose of this study was to determine if teratogenic side effects of VPA could be linked to its HDAC inhibition ability by studying a large set of structurally diverse derivatives based on the VPA core structure. We demonstrate that only VPA derivatives with a teratogenic potential in mice are able to induce a hyperacetylation in core histone H4 in teratocarcinoma F9 cells. We also demonstrate that this marker of functional HDAC inhibition occurs almost immediately (15 min) after exposure of F9 cells to VPA, whereas no influence on the HDAC protein levels (HDAC 2 and HDAC 3) could be detected even after 24 h of treatment. Further measurement of the IC50(HDAC) values of VPA derivatives in a human HDAC enzyme test system revealed an activity range from 10 to 10 000 microM; in some derivatives, HDAC inhibition ability was 40 times that of VPA. We also show a quantitative correlation between the IC50(HDAC) and the teratogenic potential of VPA derivatives, which clearly points toward HDACs as the formerly described teratogenic receptors of VPA-induced neural tube defects (NTDs).