The potential use of polymerase chain reaction (PCR)-generated DNA fragments (PCR-DNAs) as pharmaceutical agents has previously been suggested, with the demonstration of the in vitro cellular internalization and biologic activity of PCR-DNA decoy molecules targeted to human estrogen receptor gene. In order to provide information on the stability of these double-stranded DNA molecules, the nuclease resistance of PCR-DNAs of different sizes was studied in different conditions and experiments. Simulating in vitro and in vivo transfection protocol, we demonstrated that PCR-DNAs exhibited good stability toward fetal bovine serum (FBS) and adult human serum nuclease digestion. In addition, when the protective activity of liposome-based formulations toward nuclease digestion was tested, it was shown that the stability of PCR-DNAs could be further increased (up to 7 days) when a liposome-mediated delivery system was employed.