A capillary-based flow system has been developed for conducting microscale organic synthesis with the aid of microwave irradiation. The capillary internal diameter investigated ranged from 200 to 1200 mu m, while the flow rate was varied between 2 and 40 mu L/min, which corresponds to the sample being irradiated approximately 4 min. Other parameters investigated include reaction concentration and power setting of the microwave. Excellent conversion was observed in a variety of cross coupling and ring-closing metathesis (RCM) reactions employing metal catalysts and in nucleophilic aromatic substitution and Wittig reactions that do not employ metals. Reactions that have solids in them do not seem to pose a significant concern for the method, such as blocked channels. It was shown that capillaries coated internally with thin films of Pd metal show tremendous rate accelerations and that the thin films themselves are capable of catalyzing Suzuki-Miyaura reactions with no exogenous catalyst added. Importantly, it has been demonstrated that reagents in separate syringes can be coinjected into the capillary, mix, and react with none of the laminar flow problems that plague microreactor (lab on a chip) technology. This paves the way to use microwave-assisted, flow capillary synthesis as a powerful and efficient means to replace "one-at-a-time" microwave synthesis to provide libraries of compounds in a scale suitable for biological screening purposes.