Novel oxygen-incorporated SAHA (oxa-SAHA) analogues, in which oxygen was inserted in the alkyl linker connecting the hydroxamic acid moiety and amide group, were synthesized and their inhibitory activities on histone deacetylase were evaluated. The most active oxa-SAHA analogue potently inhibited histone deacetylase, almost as potently as SAHA. Various structural modifications in the amide, but not the hydroxamic acid, significantly affected the inhibitory activities of the derivatives. Based on the inhibitory data, the N-phenyl moiety of the amide turned to be a better modification site for enhancing the inhibitory activity.