We have demonstrated purification of proteins in a simple aqueous two-phase extraction process in a microfluidic device. The laminar flows inherent to microchannels allows us to perform a binary split of a complex cell lysate sample, in an open channel with no chromatography support and no moving parts. This mild process allows recovery of functional proteins with a modest increase in purity. Aromatic-rich fusion tags are used to drive partitioning of enzymes in a generic PEG-salt two-phase system. Addition of affinity ligands to the PEG phase allows us to exploit other popular fusion tags, such as polyhistidine tags and GST-tags.