BACKGROUND: Bacteriophage M13 is an Escherichia coli-specific non-lytic filamentous virus commonly used in applications ranging from antibody screening and nanomaterial construction to drug delivery, among others. In this tenor, alternative methods for the fractionation, recovery and partial purification of phage particles are desired. In this work, the use of aqueous two-phase systems (ATPS) was evaluated as an alternative method for the recovery of phage particles. RESULTS: The partition behavior of M13 in PEG-salt and ionic liquid (IL)-salt ATPS was characterized using a pre-purified feedstock. In PEG-salt ATPS, M13 was preferentially partitioned to the interface. In IL ATPS, however, M13 showed a high-top phase preference with recovery yields above 65%. Selected systems were tested for the extraction of M13 from a crude fermentation broth. From crude broth, a PEG 400-potassium phosphate system with volume ratio (V-R) of 1 and 25% w/w tie line length (TLL) gave the best M13 top phase recovery (83%) and purification fold (18.2) in terms of total protein concentration. CONCLUSIONS: The results presented here demonstrate the practical application of ATPS as an efficient process for the primary recovery and partial purification of M13 and represent the first study of the extraction of viral particles directly from a crude broth as well as the use of IL-Salt ATPS. (C) 2017 Society of Chemical Industry