The high-temperature synthesis of CdSe nanocrystals in nanoliter-volume droplets flowing in a perfluorinated carrier fluid through a microfabricated reactor is presented. A flow-focusing nanojet structure with a step increase in channel height reproducibly generated octadecene droplets in Fomblin Y 06/6 perfluorinated polyether at capillary numbers up to 0.81 and with a droplet:carrier fluid viscosity ratio of 0.035. Cadmium and selenium precursors flowing in octadecene droplets through a high-temperature (240-300 degrees C) glass microreactor produced high-quality CdSe nanocrystals, as verified by optical spectroscopy and transmission electron microscopy. Isolating the reaction solution in droplets prevented particle deposition and hydrodynamic dispersion, allowing the reproducible synthesis of nanocrystals at three different temperatures and four different residence times in the span of 4 h. Our synthesis of a wide range of nanocrystals at high temperatures, high capillary numbers, and low viscosity ratio illustrates the general utility of droplet-based microfluidic reactors to encapsulate nanoliter volumes of organic or aqueous solutions and to precisely control chemical or biochemical reactions.