Although the opioid analgesics such as morphine represent an important class of agents for the treatment of severe clinical pain, the development of tolerance and dependence often overshadows the therapeutic advantages of morphine and related opioids in individuals undergoing long-term treatments. The mechanisms underlying opioid tolerance are not fully understood, but appear to be comprised of two types of plasticity or counter-adaptation, at the cellular level and through neuronal circuits. Current studies mostly emphasize the cellular adaptation mechanisms, which include altered gene expression and receptor desensitization due to phosphorylation and endocytosis. However, the mechanisms underlying opioid tolerance and dependence are not always explained by cellular adaptation mechanisms alone. This review focuses on the plasticity in neuronal circuits achieved through an enhancement of so-called anti-opioid glutamate/NMDA receptor synaptic activities. There have been also conceptual advances in understanding the changes to supporting systems, which include the altered expression of key molecules regulating the anti-opioid system through neuron-glial networks. We also introduce a new approach using in vivo electroporation to identify the brain loci responsible for morphine tolerance and dependence.