Recent progress in molecular biology introduced a concept of molecular targeting therapy against many diseases including neurosurgical disorders. Molecular targeting therapy is promising, because targeting a disease-specific molecule it may provide cure without inducing unfavorable side effects. Focusing mainly on CNS (central nervous system) malignancies, authors discuss the current development of molecular targeting therapy with a special concern to strategies using DNA, RNA, immunotoxin, and molecular selective inhibitors. Strategies using DNA include gene therapy and DNA vaccine. RNA interference (RNAi) is one of the promising molecular targeting strategies using RNA. Immunotoxins such as recombinant chimeric cytotoxin consisting of interleukin-13 and a truncated exotoxin produced by the Pseudomonas aeruginosa bacterium is now under clinical investigation. Many molecular targeted agents such as selective inhibitors for protein kinases are now in preclinical and clinical development for patients with malignant glioma. Additionally, authors introduce their attempts to visualize the local drug delivery using real-time MRI monitoring. Visualization of drug delivery, while achieving effective drug distribution using convection-enhanced delivery (CED), may also contribute to the disease targeting. These strategies together should help us develop the effective 'disease-targeting therapy' for CNS disorders.