Conditional transgenic animals are useful tools that can be used to determine the detailed anatomic and molecular bases of sleep–wake regulation. This short review highlights some of the most recent molecular biological technologies for “systems‐level” sleep research in freely behaving animals. These technical advances include a wide range of approaches from conditional deletion of genes based on the Cre/loxP technology to RNA interference to the in vivo reversible manipulation (silencing and activation) of neurons by tetracycline‐controlled tetanus neurotoxin or the expression of genetically modified receptor‐channel complexes. In combination with these advanced genetic techniques, adeno‐associated viral vectors (AAVs) represent a versatile gene delivery system for stereotaxic‐based brain microinjections and regionally restricted transduction of neuronal cell populations.