The electrophoretic extraction of ions from a hydrodynamic flow stream is investigated at an intersection between two microfluidic channels. A pressure gradient is used to drive samples through the main channel, while ions are electrophoretically extracted into the side channels. Hydrodynamic restrictors and a neutral coating are used to suppress bulk flow through the side channels. A theoretical model that assumes Poiseuille flow in the main channel and neglects molecular diffusion is used to calculate the extraction efficiency, η, as a function of the ratio, R, of the average hydrodynamic velocity to the electrophoretic velocity. The model predicts complete extraction of ions (η = 1) for R < 2/3 and a monotonic decrease in η as R becomes greater than 2/3, which agrees well with the experimental results. Additionally, the model predicts that the aspect ratio of the microfluidic channel has little effect on the extraction efficiency. It is anticipated that this device can be used for on-line process monitoring, sample injection, and 2D separations for proteomics and other fields.