Despite evidence supporting methadone substitution treatment (MST), methadone itself has been associated with drug-related deaths. A recent external review of methadone services in Ireland concluded that Ireland is currently lacking a systematic approach of data linkage which is essential to determine the quality of care delivered to drug users in treatment, particularly in relation to mortality. The National Drug Strategy 2009-2016 also concluded that clinical research is underdeveloped. Understanding progression pathways in treatment and qualitative research regarding service users’ experiences were identified as research priorities. The proposed study aims to inform evidence-based treatment guidelines to reduce the risk of mortality associated with MST and to provide a better understanding of progression pathways within the addiction services. Using a sequential mixed methods study design, the project will involve a record linkage cohort study of approximately 3,000 patients attending specialist addiction outpatient services in Dublin South West between 2010 and 2015. The primary objectives of this cohort study are: (1) to investigate the extent to which the impact of MST on mortality (all cause and drug-related) is influenced by modifiable treatment related factors such as treatment modality, dose, treatment duration, co-prescriptions including benzodiazepines and dispensing arrangements including supervised methadone consumption; (2) to identify determinants of time to progression to treatment in primary care or detoxification; and (3) determinants of time to discontinuation in MST. This will be combined with in-depth qualitative interviews with 40 drug users in relation to their treatment pathways or journey to-date, experiences of non-fatal overdose, poly-drug use and supervised methadone consumption. Evidence generated from this study will inform both national and international policy decisions in relation to improving quality of care in MST and reducing mortality. This study will also inform evidence based initiatives around progression pathways, taking the service users perspective into account.