Microwave irradiation has become a widely accepted unconventional energy source for performing organic reactions. Microwave heating is very attractive for chemical applications as it produces a rapid and volumetric heating of samples that depends strongly on the properties of the material. In contrast, conventional heating is slow, superficial and less dependent on the properties of the material. In the period following the pioneering work of Gedye and Giguere, numerous reactions were carried out in domestic microwave ovens due to the spectacular accelerations observed in many cases. Reactions were performed under uncontrolled conditions and this led to conditions that were not easily reproduced and, in certain cases, false effects involving microwave irradiation were described. Microwave chemistry and its related instrumentation were developed as a result of the efforts of many pioneers, who believed that this technology would represent the bunsen burner of the 21st century and provide an alternative to conventional heating to obtain results that are not achieveble under other conditions. In particular, the work of Loupy in France, Strauss in Australia and Varma in the United States are worth highlighting. The increasing number of related publications in recent years - particularly since 2003 - could be related to this work and the general availability of new and reliable microwave instrumentation in which almost all of the reaction parameters can be controlled. At this moment, any chemical transformation known can be performed under microwave irradiation, at temperatures ranging from -80 to 300 °C or more, and this methodology can be combined with other techniques such as, for example, photochemistry, electrochemistry and ultrasound, or employed in conjuntion with sustainable solvents like water and ionic liquids. A large number of reactions and conditions have been described in organic synthesis: cycloaddition reactions, synthesis of radioisotopes, Fullerene chemistry, Polymers, Heterocyclic chemistry, carbohydrates and natural products, Medicinal Chemistry, Combinatorial Chemistry and High Throughput Chemistry, solvent-free reactions, homogeneous and heterogeneous catalysis, Green Chemistry and, more recently, this approach has been extended to proteomics and biological chemistry. Microwave-Assisted Organic Synthesis is characterised by the rapid heating induced by the radiation, which cannot be reproduced by classical heating. Higher yields, milder reaction conditions and shorter reaction times can be obtained and many processes can be improved. Indeed, even reactions that do not occur by conventional heating can be performed using microwaves, especially when the reaction requires the use of harsh conditions or involves sensitive reagents and/or products. The effect of microwave exposure results from material/wave interactions. These effects are highly dependent on the properties of the material and produce thermal effects (which may be easily estimated by temperature measurements) and probably specific (i.e., not purely thermal) effects. This selective mode of heating sometimes produces interesting modifications in the selectivity. Microwave reactions are characterised by short reaction times and by clean reactions, a factor that often simplifies the work-up procedure. In addition, microwave systems can be easily automated both in terms of sample preparation and analysis. These characteristics make it the technology of choice when High Throughput Chemistry is required. Further developments in microwave reactors and appropriate instrumentation for Combinatorial and High Throughput Chemistry will in future improve the utility of microwave chemistry. The aim of this special issue, included in two parts (Vol. 10, No. 9 and Vol. 10, No. 10), is to show some of the most recent advances in the field of Microwave Assisted High Throughput Chemistry. Eleven contributions from highly prestigious research groups have been selected to cover a wide range of applications of microwave chemistry in this field; including Heterocycles, Fullerenes and nanotubes, Medicinal Chemistry, Proteomics, Parallel reactions, Solid-Phase reactions and Flow conditions.