In mature lymphoid malignancies, aberrant acetylation status has been strongly linked to their tumorigenesis. Thus, the modulation of acetylation through targeting histone deacetylases (HDACs) is considered to be a viable therapeutic strategy. Vorinostat (SAHA) is the first HDAC inhibitor for the patients with cutaneous T-cell lymphoma (CTCL). Most of CTCL, ATLL and MM cells were found to be sensitive to this drug. Therefore, we established five SAHA-resistant cell lines, IC50 of the SAHA-resistant cells was 4-to 14-fold higher than that of their parental cells. Regarding HDAC activity, it was greatly inhibited by SAHA in parental cells, whereas it was only partly inhibited in SAHA-resistant cells. Next we performed microarray, results indicated that the expression level of HDAC3 being obviously low in resistant cells, which was also confirmed by real-time PCR and western blot, while other HDAC expression remained unchanged. We assumed that HDAC3 could be a main target of SAHA. To examine this possibility, we established both HDAC3 knocked-down and over-expressing cell lines, and examined the sensitivity of these cells to SAHA. HDAC3 knocked-down cells showed obviously SAHA-resistant feature, however, HDAC3 over-expressing cells showed higher sensitivity to SAHA. Thus, our results suggest that SAHA induced apoptosis depends on the inhibition of HDAC3. Finally, we supposed that HDAC3 expression was epigenetically silenced by promoter methylation in SAHA resistant cells, and attempted to restore HDAC3 expression in the presence of 5-azacytidine, a DNA demethylase. We confirmed that HDAC3 expression was restored during 6-9 days after exposure to 5-azacytidine. When HDAC3 expression being restored, the resistant cells showed higher sensitivity to SAHA. It suggests that hyper-methylation of promoter sequences of HDAC3 contributed to the mechanism of SAHA-resistance. From these results and HDAC3 might provide a useful biomarker for identifying favorable response to HDAC inhibitors, and the overcoming the resistance of HDAC inhibitors.