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Summary Background Heroin-assisted substitution treatment for severely opioid-dependent drug users has been available in Switzerland since 1994. Our aim was to ascertain the feasibility, safety, and efficacy of this treatment. Methods We did a cohort study in 21 community outpatient treatment centres. We assessed 1969 opioid-dependent drug users, who began heroin-assisted substitution treatment between January, 1994, and December, 2000, to ascertain admission and discharge patterns, and patient characteristics. We also followed up a subset of 237 patients who began treatment between Jan 1, 1994, and March 31, 1995, and who stayed with the programme for at least 18 months. We used questionnaires, interviews, and medical examinations done at entry and after 6, 12, and 18 months to assess somatic and mental health, social integration, and treatment outcomes. Findings More than 70% (1378) of patients remained in treatment for more than a year. Treatment showed positive effects with respect to health and social outcomes. A long stay in treatment was related to a higher chance of starting abstinence-oriented therapy than a short stay. Interpretation Heroin-assisted substitution treatment might be an effective option for chronically addicted patients for whom other treatments have failed.