This paper presents an integrated process for the primary recovery of intracellular glyceraldehyde 3-phosphate dehydrogenase (G3PDH) and other proteins from bakers' yeast wherein cell disruption and aqueous two-phase systems (ATPS) were operated simultaneously. Polyethylene glycol and potassium phosphate were added to the cell suspension before disruption such that the bead mill was exploited as both cell disrupter and product extractor. The partition behaviour of both bulk protein and G3PDH for the integrated process was similar to that for a conventional process in which cell disruption and ATPS extraction were operated as discrete unit operations. The target products concentrated in the upper phase for all the systems evaluated. However, the cell debris generated during the integrated process also concentrated in the upper phase which limited the potential application of the system. Subsequent evaluation of the variation of system volume ratio (V-r) with the partition behaviour of cell debris recommended process conditions (i.e. PEG 12% (w/w), phosphate 28% (w/w), V-r = 0.45, pH = 7.0) suitable for the primary recovery of intracellular proteins from debris. The results are discussed in the context of the practical potential of the direct integration of ATPS with cell disruption processes.