Abstract Background Not much is known about the health seeking behavior of people with substance use disorders before they enter specialized treatment and afterwards. This paper explains in detail the protocol that has been followed to establish the Belgian TDI-IMA-database, which is linking two separate databases: the Treatment Demand Indicator (TDI) and the database of the Intermutualistic Agency (IMA). The Treatment Demand Indicator is measuring incidence of people with substance use disorders entering drug treatment. The IMA-database covers data, collected in the framework of the compulsory Belgian health care and benefits insurance program, on reimbursed medication and the use of reimbursed health services. The linkage results in pharmacoepidemiological and health service data for people who were in treatment for substance use disorders and for a group of comparators. Methods The TDI-database was linked to the IMA-database for the period between 01/01/2008 and 31/12/2017, based on the national identification number of patients who have been in alcohol or drug treatment between 01/01/2011 and 31/12/2014. Through this linkage, pharmacoepidemiological and health service data became available for at least 3 years before the first registered episode in the TDI-database till at least 3 years after the first episode. For each person in TDI four comparators, who were not in specialized treatment, were matched on age, sex and place of residence. Discussion The TDI-IMA-database allows for an analysis of health seeking behavior and health care pathways of people before and after they entered specialized alcohol and drug treatment. The presented protocol could be used in other European countries to establish a linkage between existing health databases. This will allow for a better understanding of the health care needs of patients with substance use disorders.