Hydrogen sulfide (H2S) together with polysulfides (H2Sn, n>2) are signaling molecules like nitric oxide (NO) with various physiological roles including regulation of neuronal transmission, vascular tone, inflammation, oxygen sensing etc. H2S and H2Sn diffuse to the target proteins to S-sulfurate their cysteine residues to induce the conformational changes to alter the activity. On the other hand, 3-mercaptopyruvate sulfurtransferase transfers sulfur from a substrate 3-mercaptopyruvate to the cysteine residues of acceptor proteins. A similar mechanism has also been identified in S-nitrosylation. S-sulfuration and S-nitrosylation by enzymes proceed only inside the cell, while reactions induced by H2S, H2Sn and NO even extend to the surrounding cells. Disturbance of signaling by these molecules as well as S-sulfuration and S-nitrosylation causes many neuronal diseases. This review focuses on the signaling by H2S and H2Sn with S-sulfuration compared with those of NO and S-nitrosynation, and discuss on their roles in physiology and pathophysiology.