The authors used thermally induced surface tension gradients to manipulate aqueous droplets in microchannels. Control of the droplet breakup process was demonstrated. Droplet sorting can be achieved with temperatures above a critical value. Numerical simulation using a two-dimensional model agrees qualitatively well with the experimental results. The used control temperature of less than 55 °C shows that this active control concept is suitable for biochemical applications. Thermal control promises to be a simple and effective manipulation method for droplet-based lab on a chip.