We report on the fabrication of microfluidic channels in fused silica using femtosecond laser irradiation followed by chemical etching. Using an astigmatically shaped beam, we achieve microchannels with circular cross section and length up to $1.5\mathrm{mm}$ . We use the same femtosecond laser, with different irradiation parameters, to fabricate high quality optical waveguides on the same substrate. The integration of microchannels and waveguides will enable a forthcoming class of biophotonic sensors.