Atypical teratoid/rhabdoid tumor (ATRT) is a highly malignant central nervous system neoplasm that primarily occurs in children less than 3 years of age. Because of poor outcomes with intense and toxic multimodality treatment, new therapies are urgently needed. Histone deacetylase inhibitors (HDIs) have been evaluated as novel agents for multiple malignancies and have been shown to function as radiosensitizers. They act as epigenetic modifiers and lead to re-expression of inappropriately repressed genes, proteins, and cellular functions. Because of the underlying chromatin remodeling gene mutation in ATRT, HDIs are ideal candidates for therapeutic evaluation. To evaluate the role of HDIs against ATRT in vitro, we assessed the effect of drug treatment on proliferation, apoptosis, and gene expression. In addition, we examined HDI pretreatment as a radiosensitization strategy for ATRT. 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium with phenazine methosulfate electron coupling reagent (MTS) and clonogenic assays demonstrated that HDI treatment significantly reduces the proliferative capacity of BT-12 and BT-16 ATRT cells. In addition, the HDI SNDX-275 was able to induce apoptosis in both cell lines and induced p21(Waf1/Cip1) protein expression as measured by Western blot. Evaluation of differential gene expression by microarray and pathway analysis after HDI treatment demonstrated alterations of several key ATRT cellular functions. Finally, we showed that HDI pretreatment effectively potentiates the effect of ionizing radiation on ATRT cells as measured by clonogenic assay. Our findings suggest that the addition of HDIs to ATRT therapy may prove to be beneficial, especially when administered in combination with current treatment modalities, such as radiation.