Rapid advances in viral genomics, gene function and regulation, as well as in rational drug design, have led to the development of gene-based drugs that can induce protective antiviral immunity, interfere with viral replication, suppress viral gene expression or cleave viral mRNAs. Several such drug candidates have been developed in recent years against various viruses including HIV. Although gene-based agents show promise as anti-viral agents their therapeutic efficacy may be restricted by limited delivery to intracellular sites of viral replication and in vivo nuclease degradation. Enhancement of the efficacy of gene-based drugs by encapsulation within liposomes or insertion within viral vectors has been evaluated. This review will highlight recent developments in delivery systems used to target nucleic acid-based drugs into sites of viral replication, therefore avoiding potential drug toxicity in non-viral infected organs. Liposomeencapsulation and insertion of nucleic acid-based drugs within viral vectors can significantly enhance antiviral efficacies. Viral vector-mediated therapy usually results in greater expression of the gene-based drug than with liposome delivery, however significant safety concerns have been raised in regards to viral vector therapies. Research is ongoing to increase drug delivery to the desired target cells while eliminating adverse side effects.