Abstract Histone deacetylase inhibitors (HDACi) have been developed as anti-tumor agents and they may play a role in reversing drug resistance by combination treatment with other chemotherapeutic drugs. However, it has also been reported that HDACi can upregulate the cancer stem surface marker expression and promote stem cell self-renewal, which may cause inherit resistance to chemotherapeutic drugs. We investigated the effect of HDACi treatment on the stemness gene expression in drug resistant cells. Using SK-N-Be2C, high aggressive I type human of neuroblastoma cells, and SKN-SH, low aggressive mixed N and S type of human neuroblastoma cells, our laboratory generated doxorubicin drug resistant cell lines with and without intermittent histone deacetylase inhibitor Vorinostat treatment over one year. For each cell line, four groups were generated: wild type (WT), doxorubicin resistant (DoxR), vorinostat treated WT (WT-v), and vorinostat - treated doxorubicin resistant (DoxR-v). The cells’ sensitivity to chemotherapeutic drugs, the ability of forming tumorspheres and in vitro invasion were examined. Cell surface markers and side populations were analyzed by flow cytometry. The differential expressed stemness genes were identified by whole genome analysis and confirmed by real-time PCR. Vorinostat increased the sensitivity of SK-N-Be2C resistant cells to chemotherapy, made the cells lose the ability to form tumorspheres, and reduced in vitro invasion ability and the percentage of side population. In contrary, vorinostat decreased the sensitivity of SK-N-SH resistant cells to drugs, enhanced the cell's ability to form tumorshperes and had little effect on the cells’ invasion and side population. The putative neuroblastoma marker, CD133, was not enriched in either long term or short term vorinostat/doxorubicin treatment. Nine stemness linked genes (ABCB1, ABCC4, LMO2, SOX2, ERCC5, S100A10, IGFBP3, TCF3 and VIM) were upregulated in doxorubicin resistant SK-N-Be2C cells, compared to vorinostat - treated resistant cells. Vorinostat did not have significant effect on stemness gene expression in SK-N-SH cells, except for ABCB1 and ABCC4 genes, which were deregulated in vorinostat - treated resistant cells. In conclusion, Histone deacetylase inhibitor differentially regulates stemness gene expression in neuroblastoma drug resistant cells. It has better effect on reversing drug resistance in high aggressive neuroblastoma and this may be associated with downregulated stemness gene expression. This work may be valuable for clinicians to design treatment protocols specific for different neuroblastoma patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3365. doi:1538-7445.AM2012-3365