Nitric oxide (NO) is a gaseous molecule produced by NO synthase (NOS) and plays essential functions via S-nitrosylation. In the course of screening for the target proteins of NO, we identified histone deacetylase 6 (HDAC6). HDAC6 plays key roles in regulating cell motility and signaling through deacetylation of substrate proteins such as alpha-tubulin. In the present study, we attempted to elucidate the role of NO on HDAC6 activity. Using biotin-switch assay, we found that HDAC6 is S-nitrosylated by both NO donors and NO derive from the inducible type of NOS in A549 cells treated with inflammatory cytokines. Next, we analyzed whether NO influences on enzymatic activity of HDAC6. In vitro assays showed that treatment with S-nitrosocysteine, a physiological NO donor, significantly attenuated deacetylase activity, indicating that NO directly inhibits catalytic activity of HDAC6. Then, we examined whether NO acts on endogenous HDAC6 activity in A549 cells. The level of acetylated alpha-tubulin was significantly elevated upon treatment with cytokines, but this increment was strongly suppressed with L-NAME, a NOS inhibitor. These findings suggest that S-nitrosylation of HDAC6 plays a pivotal role in the regulation of protein acetylation.