The mechanism by which drugs that target nucleic acids cause neurotoxicity is not well described. We characterized the neurotoxicity of Hoechst 33342 (bis-benzimide), a common cell permeable nuclear dye, in primary neuronal cultures. The mechanism of cell death was not apoptotic, as death is rapid, not accompanied by typical nuclear morphological changes, and is insensitive to inhibitors of transcription, translation and caspase activity. In addition, free-radical scavenging agents failed to attenuate cell death, and damage was not accompanied by mitochondrial dysfunction. Neuronal processes of cells exposed to Hoechst 33342 display dramatic fragmentation prior to cell death. When this compound was applied selectively to the distal axons of sympathetic neurons grown in compartmented cultures, the distal axons were destroyed. However, the proximal processes present in the cell body compartment were spared, demonstrating direct axonal toxicity rather than a remote effect of nuclear dysfunction. Other cell-permeable nucleic acid binding dyes similarly caused rapid dendritic and axonal toxicity. The hypothesis that these nucleic acid binding dyes target RNA localized to dendrites and axons is supported by observations that RNaseV1 induced similar, rapid neurite fragmentation. We conclude that the neurotoxic effects of nucleic acid binding compounds are mediated, at least in part, by direct neurite injury, which does not require involvement of the cell body and nucleus.