Acyclic nucleoside phosphonate (ANP) analogues are a class of compounds with potent activity against herpesviruses and/or retroviruses. Our preliminary experiments have shown that 9-(2-phosphonylmethoxyethyl)adenine (PMEA), a prototype of the ANP family, enhances some parameters of natural immunity. In this paper we have evaluated the effect of different schedules of administration of PMEA and other ANP analogues of clinical interest upon natural killer (NK) activity and interferon (IFN) production in a mouse model. The results show that PMEA significantly enhances NK activity and interferon production. Other ANP analogues tested in our system, i.e., 9-(2-phosphonylmethoxyethyl)-2,6-diaminopurine (PMEDAP), and 9-(3-fluoro-2-phosphonylmethoxypropyl)adenine (FPMPA), similarly induced enhancement of natural immunity. The immunomodulating effect of PMEA was even more pronounced with a single administration compared to repeated administrations of the drug. Dose-dependent enhancement of NK activity and IFN production could also be demonstrated during chronic administration of PMEA (more resembling to what will be the schedule of administration of this drug in patients). Overall, the data here presented suggest that the enhancement of some natural immune functions induced by ANP analogues may add to the direct antiviral activity of these drugs against retroviruses and herpesviruses, and thus may be able to increase the host resistance against viral infections.