Abstract: This research describes the partitioning in PEG/phosphate systems of the plasmid pD2, a dengue 2 plasmid DNA vaccine, present in a clarified E. coli alkaline lysate. Factors that affect the partition as PEG molecular weight, plasmid concentration and the lysate volume loaded in the system were investigated. Results showed that partition behavior of plasmid DNA depends on the system molecular weight, a considerable amount of protein of the cell lysate was accumulated in the interphase of the systems. The best recovery plasmid yield (37%) was obtained with PEG 400 (20/20% w/w) systems with a 60% (w/w) lysate load.