In 2003, a randomised controlled trial (RCT) comparing injected diacetylmorphine and oral methadone was carried out in Andalusia, Spain. The subsequent follow-up study evaluated the health and drug use status of participants, 2 years after the completion of the trial. This follow-up cohort study was carried out between March and August 2006. Data collected included information on socio-demographics, drug use, health and health-related quality of life. Patients who received HAT showed better outcomes compared with those not on HAT. The results of this study strengthen the evidence showing that HAT can improve and stabilise the health of long-term heroin users with severe comorbidities and high mortality.