Molecules able to modulate the levels of endogenous free radicals, such as reactive oxygen species (ROS) and nitric oxide (NO), are of pivotal interest for pharmacological and pharmaceutical sciences because of their potential therapeutic relevance. In fact, ROS and NO, which are normal products of cell metabolism, may play a dual beneficial/deleterious role, depending on local concentration and mode of generation. As such, they have been identified as key pathogenic factors for many inflammatory, vascular dysfunctional and degenerative disorders, including atherosclerosis, hypertension, cardiovascular and neurodegenerative diseases, cancer, diabetes mellitus, and ageing. Therefore, the identification and characterization of novel antioxidant/free radical scavenger molecules may expand the current therapeutic implements for the treatment and prevention of the above diseases. In this perspective, low molecular weight complexes of transition metals with organic scaffolds are viewed and investigated as promising pharmaceutical agents. These complexes take advantage of the known principles of inorganic chemistry, i.e. the ability of transition metals, Fe(II), Co(II), Mn(II) and Ru(II), to bind to and react with NO and/or ROS, to counterbalance excessive endogenous free radical generation in biological systems. Among NO scavengers, representative examples are iron complexes with dithiocarbamates or ruthenium compounds with polyamine-polycarboxylate scaffolds; on the other hand, manganese-based molecules appear effective as ROS scavengers. Of note, Mn(II)-containing molecules, currently under study as ROS scavengers, have major functional similarities to Mn-superoxide dismutase (SOD), a Mn-containing enzyme acting as potent endogenous anti-oxidant. In this article, we briefly summarize the state-of-the-art concerning the chemical and biological properties of transition metal ion complexes with low molecular weight synthetic ligands as ROS/NO scavengers provided with therapeutic effectiveness in animal models of free radical-induced diseases. A proper design of the organic scaffolds may yield metal complexes which are stable in aqueous solution in a wide range of physical and chemical conditions, thus preventing release of the metal and the related toxicity. These metal-based compounds may be viewed as a novel class of drugs helpful to reduce vascular dysfunction and oxidative tissue injury due to derangements of the endogenous generation/catabolism of NO and ROS.