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Scientific information about the neurobiology of addictive behaviors provides an increasingly important rationale to support opioid agonist pharmacotherapy, primarily methadone maintenance treatment, for long-term heroin addiction. In late 1963 and 1964, the first research was performed at The Rockefeller Institute for Medical Research by Dole, Nyswander, and Kreek in an attempt to develop a new pharmacotherapy for opiate addiction. The hypothesis underlying that research was that heroin addiction was a disease. However, the evidence for heroin addiction being a disease was based primarily on clinical anecdotes and the natural history of opiate addiction. Until then chronic addiction was managed primarily using abstinence-based, medication-free behavioral approaches. Such approaches were uniformly successful in only a small percent of long-term heroin addicts. Subsequent research, both clinical research as well as laboratory-based research, using a variety of appropriate animal models as well as in vitro techniques, has shown that drugs of abuse in general, and specifically the short-acting opiates, such as heroin, may profoundly alter molecular and neurochemical indices, and thus physiologic functions. Also, research has shown that after chronic exposure to a short-acting opiate,these alterations may be persistent, or even permanent, and may contribute directly to the perpetuation of self-administration of opiates, and even the return to opiate use after achieving a drug-free and medication-free state. There is ample evidence now that disruption of several components of the endogenous opioid system, ranging from changes in gene expression to changes in behavior, may occur during cycles of short-acting opiate abuse. Also, there are very convincing studies that suggest that stress responsivity is profoundly altered by chronic abuse of short-acting opiates including: documentation of atypical hypo-responsivity to stressors during cycles of heroin addiction; evidence of sustained hyper-responsivity to stressors in the medication-free, illicit-opiate-free state; and in contrast, normalization of stress responsivity, as reflected by the hypothalamic-pituitary-adrenal axis function in long-term, methadone-maintained patients. Thus, both laboratory and clinical research studies provide firm documentation that the disruption of physiologic, as well as behavioral, functions occurs during chronic administration of short-acting opiates. Also, there is research evidence of an epidemiologic, and more recently of a molecular genetics type, that a genetic vulnerability to develop addictions in general, and opiate addiction specifically, may exist, and that early environmental factors may alter physiology to enhance vulnerability to develop opiate addiction when self-exposed.