Contamination by cell debris and non-viable cells is common in cell-based processes. Cell fragments and dead cells can be produced during culture and in purification steps, and often must be eliminated before analyses, subsequent process steps, and/or final application to avoid interference, fouling and reduced product yields. In the present work, the selective elimination of cell debris from CD133(+) stem cells by aqueous two-phase system (ATPS) partitioning is demonstrated. Two conventional ATPS systems showed no selectivity, with 100% of both cell debris and CD133(+) stem cells partitioning to the top phase of a Ficoll 400,000-dextran 70,000 system and 100% of both debris and CD133(+) cells partitioning to the bottom phase of a PEG 8000-dextran 500,000 system. In a novel UCON-dextran 75,000 system, however, 100% of the CD133(+) stem cells partitioned to the bottom phase, while non-viable cells, cell debris and other non-mononuclear cells all partitioned to some extent to the top phase, away from the desired CD133(+) cells. CD133(+) cell viability was at least 98% after ATPS processing. This result suggests that with larger phase ratios or continuous extraction, this or related ATPS systems could remove essentially all cell debris and non-viable cells with cell yield and viability both near 100%" This approach might find application in a wide variety of cell-based technologies. (C) 2015 Elsevier B.V. All rights reserved.