The role of nitric oxide in several signalling routes has been clearly established. In recent years increasing attention has been paid to its ability to produce covalent protein post-translational modifications in conjunction with other reactive oxygen and nitrogen species. Among these, the modification of cysteine residues has been shown to be of particular importance due to the functional relevance of many of them. In this review, we focus on the modification of the cysteine thiol by incorporation of a NO moiety (S-nitrosylation) or of a glutathione moiety (S-glutathionylation). Both modifications are produced by different reactions induced by nitric oxide-related species. We discuss the differences and similarities of both modifications, and their relationships, in regard to the biochemical mechanisms that produce them, including the enzymatic activities that may catalyze some of them and their subcellular compartmentalization. Even when biochemical knowledge is one step ahead of the demonstration of their pathophysiological relevance, we also describe the potential role of both modifications in several processes in which both post-translational modifications are involved.