Few studies have investigated methadone maintenance treatment of opiate dependent patients in primary health care settings compared to specialist clinic settings. Using a prospective cohort design, the study investigated outcomes at one year for 660 patients treated by seventy general practitioners or by three drug clinics at sites across the Canton of Basel-Stadt, Switzerland. The main treatment outcome measures were: retention in treatment, attendance of consultations, prescribed methadone doses, and illicit drug use over time. Mean daily methadone dose for patients in general practice (GP) was 69.3 mg (SD = 44.7) and for patients in specialized clinics 76.7 mg (SD = 48.4). The overall one-year retention in treatment was 74% (GP, 75.6%; clinics, 72.2%). The proportion of reported concomitant heroin use was significantly lower in patients treated by GPs compared to the clinic sample (49% versus 72%; P < 0.0001), as well as the proportion of reported concomitant cocaine use (GP, 24%; clinics, 41%; P = 0.001). The same accounts for reported intravenous drug use (GP, 40% versus 58%; P < 0.0001). The concomitant use of benzodiazepines and alcohol did not differ between groups. Reductions in concomitant heroin and cocaine use were found in both groups at follow-up, by comparing admission, with average-stay and long-term samples. Patients in GP settings attended an average of 5.14 out of 6.19 scheduled consultations, patients in specialist clinic settings an average of 6.8 out of 7.86 scheduled consultations in a six-month period. The proportion of take-home medication for both groups was 69%. Comparing treatment outcome with the amount of consultations in both treatment settings, patients with a higher rate of consultations (4 to 7) had a significantly better retention rate in both groups (P = 0.002; P< 0.0001) compared to patients with a low rate of consultations (0 to 3). Results show substantial reductions in concomitant heroin use, among 'real world' patients treated in GP and in clinic settings, which were sustained at one-year follow-up. Our results support the success of methadone maintenance provided by primary care physicians' offices. Furthermore, our results provide evidence, that GPs treat an equal proportion of 'unstable patients' (25%) as do the clinics, indicating the knowledge and long clinical experience of this sample of GPs. However, providing better professional support, competence training and financial remains a goal for future developments in the primary health care field.