In Switzerland, opioid maintenance prescription for heroin dependence is possible since the seventies, by all licensed physicians, in specialized centers or primary care, and reimbursed by basic health insurance. Every treatment must be declared to the cantonal public health officer. Aim: The aim of our study was to compare basic facts, trends, and outcomes of mainly primary care based opioid maintenance treatment in two areas in Switzerland (Ticino, Geneva) with different health care organizations. Methods: Historical cohort study with data-collection (start, every 6 months, end) through standardized administrative databases. Results: Overall 3,824 patients (28% females) were included over a 3.5 years period. Of all treatment episodes 97% concerned methadone prescription. We observed an aging population, with no significant canton effect on retention in treatment. Prescribers practicing in or close to specialized centers were more compliant with methadone guidelines. Female patients were better retained in primary care settings. Conclusion: This study adds evidence for the effectiveness of opioid maintenance treatment in primary care, especially for female patients. Continuous education should be encouraged to increase congruence with guidelines.