The influence of temperature on isothermal rarefied gas flows in rectangular microchannels is experimentally investigated. A specific setup with accurate temperature regulation, by means of Peltier modules, has been designed, and the mass flowrate through long microchannels is measured using the constant volume method. The channels are etched by DRIE in silicon wafers and anodically bonded by Pyrex plates; their hydraulic diameter is of the order of one micrometer. The effect of temperature on flowrate is investigated in the range 287 to 317 K, for flows of helium. The flow is in the slip flow regime, with average Knudsen numbers of the order of 0.1. The experimental data are in very good agreement with a second-order slip flow model, with an accommodation coefficient close to unity, whatever the operating temperature.