Microwave Assisted Organic Synthesis is known for the spectacular accelerations produced in many reactions as a consequence of heating rates that cannot be reproduced by classical heating. As a result, higher yields, milder reaction conditions and shorter reaction times can be achieved and many processes can be improved. Furthermore, reactions that do not occur by conventional heating can often be carried out under the action of microwaves. This effect is particularly important in the preparation of isotopically labeled drugs with short halflives (11C, t1 / 2 = 20 min.; 122I, t1 / 2 = 3.6 min. and 18F, t1 / 2 = 100 min.) and high throughput chemistry (combinatorial chemistry and parallel synthesis). Another very important application of microwave irradiation involves the modification of the selectivity (chemo-, regio- and stereoselectivity) in relation to conventional heating. Selectivity is a crucial objective in organic synthesis and is usually achieved by selecting the appropriate reaction conditions, solvent, temperature, time or using kinetic vs. thermodynamic control, protection and activation and selective catalysts. The ability to control the selectivity by simply choosing the appropriate mode of heating (conventional vs. microwaves) is very attractive proposition. However, the effect of microwave irradiation still needs to be rationalized in order to predict the effect of the radiation on the selectivity of a given reaction.