Specific cellular and temporal regulation of gene expression is a goal of many molecular studies. The study of programmed cell death requires cellular specificity, temporal regulation, as well as the interaction of a myriad of gene products. One way to regulate these interactions in an apoptotic cell is by specifically altering gene expression using a DNA transfer system. Several methods exist that are capable of delivering gene constructs into intact animals. DNA can be introduced into cells by direct DNA transfer using liposome-encapsulated DNA or viral vector systems which carry the gene of interest. An ex vivo approach can be implemented whereby cells are manipulated to produce the desired gene product and subsequently transferred to the animal. Transfer can also be accomplished using viral vector systems. In particular, transfer into the central nervous system and neurons is most commonly accomplished using various viral vector systems. Our laboratory and others have been developing herpes simplex virus (HSV) amplicon vectors, which are plasmid-based vectors that carry the gene of interest under the control of a specific promoter. In this chapter, we will review HSV amplicon vectors as a modality for gene transfer in two models of apoptosis, central nervous system (CNS) ischemia and cochlear degeneration. Improved helper-free amplicon methodology will be described, as well as advantages and disadvantages associated with this viral vector system.