This is the first study to demonstrate an experiment-wise significant difference in DNA methylation at a specific CpG dinucleotide site between subjects with an addiction and controls at any gene. The identification of DNA methylation as a potential mechanism contributing to the development of heroin addiction, or as a result of heroin use or methadone pharmacotherapy, should lead to improved prevention or treatment of heroin addiction. Elucidation of the factors controlling DNA methylation may also help in understanding the role of the environment in this disease and its treatment.